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CHECK report for treeio on tokay1

This page was generated on 2019-04-13 11:27:25 -0400 (Sat, 13 Apr 2019).

Package 1583/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treeio 1.6.2
Guangchuang Yu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/treeio
Branch: RELEASE_3_8
Last Commit: 4fb11e8
Last Changed Date: 2019-01-25 15:18:28 -0400 (Fri, 25 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: treeio
Version: 1.6.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:treeio.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings treeio_1.6.2.tar.gz
StartedAt: 2019-04-13 06:01:31 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:03:44 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 133.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: treeio.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:treeio.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings treeio_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/treeio.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'treeio/DESCRIPTION' ... OK
* this is package 'treeio' version '1.6.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'treeio' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:34: file link 'Nnode' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:34: file link 'Ntip' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:34: file link 'is.rooted' in package 'ape' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:36: file link 'full_join' in package 'dplyr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:38: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:40: file link 'data_frame' in package 'tibble' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:42: file link 'get.fields' in package 'tidytree' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:42: file link 'get.data' in package 'tidytree' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/treeio.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/treeio.Rcheck/00check.log'
for details.

Installation output

treeio.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/treeio_1.6.2.tar.gz && rm -rf treeio.buildbin-libdir && mkdir treeio.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=treeio.buildbin-libdir treeio_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL treeio_1.6.2.zip && rm treeio_1.6.2.tar.gz treeio_1.6.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  744k  100  744k    0     0  16.7M      0 --:--:-- --:--:-- --:--:-- 18.1M

install for i386

* installing *source* package 'treeio' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'treeio'
    finding HTML links ... done
    Nnode.treedata                          html  
    as.treedata                             html  
    beast-mrbayes-parser                    html  
    drop.tip-methods                        html  
    get-placements                          html  
    get.tree                                html  
    get.treetext-methods                    html  
    getNodeNum                              html  
    is.ggtree                               html  
    jplace-class                            html  
    label_branch_paml                       html  
    mask                                    html  
    merge_tree                              html  
    phyPML                                  html  
    print.beastList                         html  
    raxml2nwk                               html  
    read-jtree                              html  
    read.astral                             html  
    read.codeml                             html  
    read.codeml_mlc                         html  
    read.fasta                              html  
    read.hyphy                              html  
    read.hyphy.seq                          html  
    read.iqtree                             html  
    read.jplace                             html  
    read.newick                             html  
    read.nhx                                html  
    read.paml_rst                           html  
    read.phylip                             html  
    read.phylip.seq                         html  
    read.phylip.tree                        html  
    read.phyloT                             html  
    read.r8s                                html  
    read.raxml                              html  
    reexports                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:34: file link 'Nnode' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:34: file link 'Ntip' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:34: file link 'is.rooted' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:36: file link 'full_join' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:38: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:40: file link 'data_frame' in package 'tibble' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:42: file link 'get.fields' in package 'tidytree' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpa4CnPc/R.INSTALLe6898e11c8/treeio/man/reexports.Rd:42: file link 'get.data' in package 'tidytree' does not exist and so has been treated as a topic
    rename_taxa                             html  
    taxa_rename                             html  
    tree_subset                             html  
    write-jtree                             html  
    write.beast                             html  
    write.jplace                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'treeio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'treeio' as treeio_1.6.2.zip
* DONE (treeio)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'treeio' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

treeio.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)
> 
> 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};",
	"data":[
  {
    "edge_num": 1,
    "subs": "C214T / G294T / T966C / C1641T / A1808G / C1941T / C2070T",
    "AA_subs": "K603R",
    "t": 0.01,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0646,
    "dN": 0.0007,
    "dS": 0.0101,
    "N_x_dN": 1,
    "S_x_dS": 6.4
  },
  {
    "edge_num": 2,
    "subs": "C222T / G555A / C732A / C828T / G939T / T999C / A1047G / G1083A / C1263T / G1329A / A1341G / A1344T / T1405C / T1440C / C1752T / A1827G / C1911T / C1941T / G2013A / T2022C / C2043T",
    "AA_subs": "",
    "t": 0.032,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0358,
    "N_x_dN": 0,
    "S_x_dS": 22.7
  },
  {
    "edge_num": 3,
    "subs": "A204G / C222T / G504A / A815G / C891T / G1023T / T1061C / G1101A / G1176A / C1299T / C1545T / C1584T / T1626C / A1668G / G1878A / G1884T / C1944T / A1947G",
    "AA_subs": "N272S / I354T",
    "t": 0.028,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0461,
    "dN": 0.0013,
    "dS": 0.0282,
    "N_x_dN": 2,
    "S_x_dS": 17.9
  },
  {
    "edge_num": 4,
    "subs": "A111G / A168G / T211C / A213G / T214C / G243A / A311G / T315A / G369A / G423A / A477C / G504A / G555A / G585A / C621T / C636T / A768G / T771C / G774A / T780C / C825T / A867G / A870G / G885A / C888T / G897A / C987T / C1006T / G1017A / A1047G / C1062T / A1146T / G1197A / A1230G / A1281G / T1365C / C1392T / T1439C / A1443G / T1512C / T1530C / T1539C / T1560C / A1608G / G1671A / G1689A / G1695A / A1761G / T1776C / T1787C / A1914G / G2052A",
    "AA_subs": "K104R / F105L / E382D / F480S / I596T",
    "t": 0.082,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0385,
    "dN": 0.0033,
    "dS": 0.0849,
    "N_x_dN": 5,
    "S_x_dS": 53.8
  },
  {
    "edge_num": 5,
    "subs": "C174T / G243A / G321A / A622T / T831C / A894G / G948T / C960T / A984G / C1041T / G1135A / T1215C / T1249C / A1401G / T1527A / T1594C / A1826G / A1848G / T1950C / G1986A",
    "AA_subs": "T208S / V379I / K609R",
    "t": 0.031,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0641,
    "dN": 0.002,
    "dS": 0.0305,
    "N_x_dN": 3,
    "S_x_dS": 19.3
  },
  {
    "edge_num": 6,
    "subs": "T829C / C1353T / A1443G / T1548C / C1645A",
    "AA_subs": "S277P / L549I",
    "t": 0.007,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.298,
    "dN": 0.0013,
    "dS": 0.0044,
    "N_x_dN": 2,
    "S_x_dS": 2.8
  },
  {
    "edge_num": 7,
    "subs": "A5T / A69G / G106T / C156T / C237T / G295A / G301C / A337C / A342G / G423T / G426T / C501T / C582T / T654C / G774A / G819C / G885T / C889T / G903A / G1191A / A1194G / A1248G / G1287A / T1405C / G1455T / C1467T / T1620C / A1674G / G1689T / T1956A",
    "AA_subs": "E2V / A36S / G99R / E101Q / K113Q / E141D / K142N / H297Y / M485I",
    "t": 0.046,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.1621,
    "dN": 0.006,
    "dS": 0.0373,
    "N_x_dN": 9.2,
    "S_x_dS": 23.6
  },
  {
    "edge_num": 8,
    "subs": "A112G / C132A / G498A / G774T / A792C / T1002C / G1020A / A1230G / A1326G / G1350T / T1527A / G1638A / C1709T / C1803A / G2103A",
    "AA_subs": "I38V / E258D / T570I",
    "t": 0.021,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.1028,
    "dN": 0.002,
    "dS": 0.0191,
    "N_x_dN": 3,
    "S_x_dS": 12.1
  },
  {
    "edge_num": 9,
    "subs": "T211C / C582T / C891T / A894G / G1083A / G1116A / C1299T / C1374T / T1530C / G1878A",
    "AA_subs": "",
    "t": 0.015,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0167,
    "N_x_dN": 0,
    "S_x_dS": 10.6
  },
  {
    "edge_num": 10,
    "subs": "G295A / A618G / A783C / C996T / G1593A / A1845G / C1944T / T1980A / C2040T",
    "AA_subs": "G99R",
    "t": 0.014,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0457,
    "dN": 0.0007,
    "dS": 0.0143,
    "N_x_dN": 1,
    "S_x_dS": 9
  },
  {
    "edge_num": 11,
    "subs": "G96A / T279C / C282T / G297A / C303T / C318A / C333T / C336T / A417G / G420A / A477G / T486C / C513A / G525A / C762T / A777T / G840A / T861C / C864T / C888T / A912G / C945T / C993T / A1053G / G1159A / T1188C / A1194G / G1197A / A1219G / C1233T / T1249C / G1294A / G1308A / A1326G / G1407A / G1470A / G1482A / T1512C / T1581C / T1623C / C1641T / C1665T / G1722A / A1761G / T1800C / A1827G / G1887A / A1920G / C1921T / A1929G / C2143T",
    "AA_subs": "V387I / I407V / V432I",
    "t": 0.082,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0224,
    "dN": 0.002,
    "dS": 0.0878,
    "N_x_dN": 3,
    "S_x_dS": 55.6
  },
  {
    "edge_num": 12,
    "subs": "G852T / G1020A / T1594C",
    "AA_subs": "",
    "t": 0.006,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0062,
    "N_x_dN": 0,
    "S_x_dS": 3.9
  },
  {
    "edge_num": 13,
    "subs": "G58A / G84A / A171T / G270A / C1680T / C1803T",
    "AA_subs": "A20T",
    "t": 0.009,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0738,
    "dN": 0.0007,
    "dS": 0.0088,
    "N_x_dN": 1,
    "S_x_dS": 5.6
  },
  {
    "edge_num": 14,
    "subs": "A126G / A171G / T207C / G243A / T321A / A342G / G369A / C405T / C483T / G504A / A537G / C804T / G810A / G909A / G1098A / G1101A / A1131G / G1137A / T1227C / A1290G / G1329A / A1518G / A1521G / C1545T / C1603T / A1608G / T1626C / T1629C / C1647A / G1671A / C1719T / G1779A / A1881G / G1971A / G2028T / A2037G / C2043T",
    "AA_subs": "H535Y",
    "t": 0.062,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0095,
    "dN": 0.0007,
    "dS": 0.0689,
    "N_x_dN": 1,
    "S_x_dS": 43.6
  },
  {
    "edge_num": 15,
    "subs": "C16A / G96A / C169A / A286C / A344G / C531T / A534C / G537A / A789T / T822A / G879A / A962T / C1005T / G1074A / A1090G / C1110T / A1125T / A1146G / C1164T / C1182T / G1239A / T1410C / T1413C / C1428T / C1473A / C1641T / T1764C / A1851G / T1932G / C1965A / A1983G / T2022C",
    "AA_subs": "N96H / N115S / N321I / S364G",
    "t": 0.048,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0538,
    "dN": 0.0026,
    "dS": 0.0485,
    "N_x_dN": 4,
    "S_x_dS": 30.7
  },
  {
    "edge_num": 17,
    "subs": "T39C / T105C / C108A / T135C / T159C / T165C / G204A / G231A / C303G / G306A / T309C / C315T / T325C / A339G / A372G / T381C / T393C / G420C / T435C / A441T / G459A / C480T / T552C / C798T / T801C / G843A / C864G / C876T / A879G / G894A / A900G / T903G / A921G / G936A / T942C / C966T / G967A / A969C / A981G / C1002T / G1023A / C1035T / A1038G / A1068G / T1110C / T1119C / G1146A / C1149T / T1161C / A1170G / G1172A / A1191G / T1198C / T1200C / G1206A / A1254T / G1260A / T1263C / T1269A / C1293T / G1317A / T1320C / A1350G / T1356C / C1398T / C1404T / T1408C / G1410C / A1425G / C1440T / G1464A / G1491A / C1527T / C1542T / C1566T / A1572G / C1575T / T1584C / C1594T / G1599A / G1632A / A1638G / A1650G / G1653A / G1716A / C1734T / G1740A / G1746A / A1749C / A1773G / C1794T / G1797A / T1803C / G1815A / A1869G / C1872A / A1878G / G1902A / A1917C / G1935A / T1974C / A1986G / T1993C / T1998A / A2013G / C2022T / T2070C / C2088T / G2112A / A2147G",
    "AA_subs": "D101E / V323I / R391K / S400P / K716R",
    "t": 0.232,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0129,
    "dN": 0.0033,
    "dS": 0.2541,
    "N_x_dN": 5,
    "S_x_dS": 160.9
  },
  {
    "edge_num": 18,
    "subs": "T144C / T182C / G187A / A210G / T237C / A294G / G297A / C318T / T321G / A540G / G783A / A785G / G814A / C948A / T1041C / A1059G / A1213T / C1215T / G1226A / C1245T / T1299C / C1405T / C1419T / G1470A / G1482A / G1500A / T1548C / C1557T / T1578C / C1605T / A1660G / C1764T / T1767C / G1791A / A1819T / T1899C",
    "AA_subs": "I61T / V63I / K262R / D272N / S405C / S409N / I554V / M607L",
    "t": 0.059,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0964,
    "dN": 0.0053,
    "dS": 0.0545,
    "N_x_dN": 8,
    "S_x_dS": 34.5
  },
  {
    "edge_num": 19,
    "subs": "G147T / T492C / A537G / T771C / A1128G / A1347G / T1497C / G1563A / C1620T / A1716G",
    "AA_subs": "",
    "t": 0.015,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0166,
    "N_x_dN": 0,
    "S_x_dS": 10.5
  },
  {
    "edge_num": 20,
    "subs": "G109T / A183T / A213G / G366A / C370A / A399G / C408T / G411A / A462G / G585A / G597A / T798C / T891C / G1009A / A1023G / C1062T / G1098A / A1134G / G1163A / T1167C / T1179C / T1305C / G1308A / C1338T / T1557C / G1572A / T1800C / T1819C / G2052A / G2145A",
    "AA_subs": "A37S / A337T / S388N",
    "t": 0.046,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0419,
    "dN": 0.002,
    "dS": 0.047,
    "N_x_dN": 3,
    "S_x_dS": 29.8
  },
  {
    "edge_num": 21,
    "subs": "C801T / A939G / A948G / G1026A / A1131G / A1267G / A1327C / G1344A / G1590A / C1686T / T1710C / G1869A / C1875T / C1893T / G2051A",
    "AA_subs": "I423V / G684E",
    "t": 0.024,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0549,
    "dN": 0.0013,
    "dS": 0.0237,
    "N_x_dN": 2,
    "S_x_dS": 15
  },
  {
    "edge_num": 22,
    "subs": "T183C / G210A / C420A / C1006A / G1116A / G1137A / C1221T / T1254C / C1410T / C1437T / C1993T",
    "AA_subs": "L336M",
    "t": 0.016,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0395,
    "dN": 0.0007,
    "dS": 0.0165,
    "N_x_dN": 1,
    "S_x_dS": 10.4
  },
  {
    "edge_num": 23,
    "subs": "T211C / T279C / G1134A / T1149C / C1179T / G1695T",
    "AA_subs": "",
    "t": 0.008,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0094,
    "N_x_dN": 0,
    "S_x_dS": 6
  },
  {
    "edge_num": 24,
    "subs": "",
    "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": "Sat Apr 13 06:03:19 2019"}
}
== testthat results  ===========================================================
OK: 125 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.82    0.31   10.34

treeio.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
> 
> 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};",
	"data":[
  {
    "edge_num": 1,
    "subs": "C214T / G294T / T966C / C1641T / A1808G / C1941T / C2070T",
    "AA_subs": "K603R",
    "t": 0.01,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0646,
    "dN": 0.0007,
    "dS": 0.0101,
    "N_x_dN": 1,
    "S_x_dS": 6.4
  },
  {
    "edge_num": 2,
    "subs": "C222T / G555A / C732A / C828T / G939T / T999C / A1047G / G1083A / C1263T / G1329A / A1341G / A1344T / T1405C / T1440C / C1752T / A1827G / C1911T / C1941T / G2013A / T2022C / C2043T",
    "AA_subs": "",
    "t": 0.032,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0358,
    "N_x_dN": 0,
    "S_x_dS": 22.7
  },
  {
    "edge_num": 3,
    "subs": "A204G / C222T / G504A / A815G / C891T / G1023T / T1061C / G1101A / G1176A / C1299T / C1545T / C1584T / T1626C / A1668G / G1878A / G1884T / C1944T / A1947G",
    "AA_subs": "N272S / I354T",
    "t": 0.028,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0461,
    "dN": 0.0013,
    "dS": 0.0282,
    "N_x_dN": 2,
    "S_x_dS": 17.9
  },
  {
    "edge_num": 4,
    "subs": "A111G / A168G / T211C / A213G / T214C / G243A / A311G / T315A / G369A / G423A / A477C / G504A / G555A / G585A / C621T / C636T / A768G / T771C / G774A / T780C / C825T / A867G / A870G / G885A / C888T / G897A / C987T / C1006T / G1017A / A1047G / C1062T / A1146T / G1197A / A1230G / A1281G / T1365C / C1392T / T1439C / A1443G / T1512C / T1530C / T1539C / T1560C / A1608G / G1671A / G1689A / G1695A / A1761G / T1776C / T1787C / A1914G / G2052A",
    "AA_subs": "K104R / F105L / E382D / F480S / I596T",
    "t": 0.082,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0385,
    "dN": 0.0033,
    "dS": 0.0849,
    "N_x_dN": 5,
    "S_x_dS": 53.8
  },
  {
    "edge_num": 5,
    "subs": "C174T / G243A / G321A / A622T / T831C / A894G / G948T / C960T / A984G / C1041T / G1135A / T1215C / T1249C / A1401G / T1527A / T1594C / A1826G / A1848G / T1950C / G1986A",
    "AA_subs": "T208S / V379I / K609R",
    "t": 0.031,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0641,
    "dN": 0.002,
    "dS": 0.0305,
    "N_x_dN": 3,
    "S_x_dS": 19.3
  },
  {
    "edge_num": 6,
    "subs": "T829C / C1353T / A1443G / T1548C / C1645A",
    "AA_subs": "S277P / L549I",
    "t": 0.007,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.298,
    "dN": 0.0013,
    "dS": 0.0044,
    "N_x_dN": 2,
    "S_x_dS": 2.8
  },
  {
    "edge_num": 7,
    "subs": "A5T / A69G / G106T / C156T / C237T / G295A / G301C / A337C / A342G / G423T / G426T / C501T / C582T / T654C / G774A / G819C / G885T / C889T / G903A / G1191A / A1194G / A1248G / G1287A / T1405C / G1455T / C1467T / T1620C / A1674G / G1689T / T1956A",
    "AA_subs": "E2V / A36S / G99R / E101Q / K113Q / E141D / K142N / H297Y / M485I",
    "t": 0.046,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.1621,
    "dN": 0.006,
    "dS": 0.0373,
    "N_x_dN": 9.2,
    "S_x_dS": 23.6
  },
  {
    "edge_num": 8,
    "subs": "A112G / C132A / G498A / G774T / A792C / T1002C / G1020A / A1230G / A1326G / G1350T / T1527A / G1638A / C1709T / C1803A / G2103A",
    "AA_subs": "I38V / E258D / T570I",
    "t": 0.021,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.1028,
    "dN": 0.002,
    "dS": 0.0191,
    "N_x_dN": 3,
    "S_x_dS": 12.1
  },
  {
    "edge_num": 9,
    "subs": "T211C / C582T / C891T / A894G / G1083A / G1116A / C1299T / C1374T / T1530C / G1878A",
    "AA_subs": "",
    "t": 0.015,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0167,
    "N_x_dN": 0,
    "S_x_dS": 10.6
  },
  {
    "edge_num": 10,
    "subs": "G295A / A618G / A783C / C996T / G1593A / A1845G / C1944T / T1980A / C2040T",
    "AA_subs": "G99R",
    "t": 0.014,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0457,
    "dN": 0.0007,
    "dS": 0.0143,
    "N_x_dN": 1,
    "S_x_dS": 9
  },
  {
    "edge_num": 11,
    "subs": "G96A / T279C / C282T / G297A / C303T / C318A / C333T / C336T / A417G / G420A / A477G / T486C / C513A / G525A / C762T / A777T / G840A / T861C / C864T / C888T / A912G / C945T / C993T / A1053G / G1159A / T1188C / A1194G / G1197A / A1219G / C1233T / T1249C / G1294A / G1308A / A1326G / G1407A / G1470A / G1482A / T1512C / T1581C / T1623C / C1641T / C1665T / G1722A / A1761G / T1800C / A1827G / G1887A / A1920G / C1921T / A1929G / C2143T",
    "AA_subs": "V387I / I407V / V432I",
    "t": 0.082,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0224,
    "dN": 0.002,
    "dS": 0.0878,
    "N_x_dN": 3,
    "S_x_dS": 55.6
  },
  {
    "edge_num": 12,
    "subs": "G852T / G1020A / T1594C",
    "AA_subs": "",
    "t": 0.006,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0062,
    "N_x_dN": 0,
    "S_x_dS": 3.9
  },
  {
    "edge_num": 13,
    "subs": "G58A / G84A / A171T / G270A / C1680T / C1803T",
    "AA_subs": "A20T",
    "t": 0.009,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0738,
    "dN": 0.0007,
    "dS": 0.0088,
    "N_x_dN": 1,
    "S_x_dS": 5.6
  },
  {
    "edge_num": 14,
    "subs": "A126G / A171G / T207C / G243A / T321A / A342G / G369A / C405T / C483T / G504A / A537G / C804T / G810A / G909A / G1098A / G1101A / A1131G / G1137A / T1227C / A1290G / G1329A / A1518G / A1521G / C1545T / C1603T / A1608G / T1626C / T1629C / C1647A / G1671A / C1719T / G1779A / A1881G / G1971A / G2028T / A2037G / C2043T",
    "AA_subs": "H535Y",
    "t": 0.062,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0095,
    "dN": 0.0007,
    "dS": 0.0689,
    "N_x_dN": 1,
    "S_x_dS": 43.6
  },
  {
    "edge_num": 15,
    "subs": "C16A / G96A / C169A / A286C / A344G / C531T / A534C / G537A / A789T / T822A / G879A / A962T / C1005T / G1074A / A1090G / C1110T / A1125T / A1146G / C1164T / C1182T / G1239A / T1410C / T1413C / C1428T / C1473A / C1641T / T1764C / A1851G / T1932G / C1965A / A1983G / T2022C",
    "AA_subs": "N96H / N115S / N321I / S364G",
    "t": 0.048,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0538,
    "dN": 0.0026,
    "dS": 0.0485,
    "N_x_dN": 4,
    "S_x_dS": 30.7
  },
  {
    "edge_num": 17,
    "subs": "T39C / T105C / C108A / T135C / T159C / T165C / G204A / G231A / C303G / G306A / T309C / C315T / T325C / A339G / A372G / T381C / T393C / G420C / T435C / A441T / G459A / C480T / T552C / C798T / T801C / G843A / C864G / C876T / A879G / G894A / A900G / T903G / A921G / G936A / T942C / C966T / G967A / A969C / A981G / C1002T / G1023A / C1035T / A1038G / A1068G / T1110C / T1119C / G1146A / C1149T / T1161C / A1170G / G1172A / A1191G / T1198C / T1200C / G1206A / A1254T / G1260A / T1263C / T1269A / C1293T / G1317A / T1320C / A1350G / T1356C / C1398T / C1404T / T1408C / G1410C / A1425G / C1440T / G1464A / G1491A / C1527T / C1542T / C1566T / A1572G / C1575T / T1584C / C1594T / G1599A / G1632A / A1638G / A1650G / G1653A / G1716A / C1734T / G1740A / G1746A / A1749C / A1773G / C1794T / G1797A / T1803C / G1815A / A1869G / C1872A / A1878G / G1902A / A1917C / G1935A / T1974C / A1986G / T1993C / T1998A / A2013G / C2022T / T2070C / C2088T / G2112A / A2147G",
    "AA_subs": "D101E / V323I / R391K / S400P / K716R",
    "t": 0.232,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0129,
    "dN": 0.0033,
    "dS": 0.2541,
    "N_x_dN": 5,
    "S_x_dS": 160.9
  },
  {
    "edge_num": 18,
    "subs": "T144C / T182C / G187A / A210G / T237C / A294G / G297A / C318T / T321G / A540G / G783A / A785G / G814A / C948A / T1041C / A1059G / A1213T / C1215T / G1226A / C1245T / T1299C / C1405T / C1419T / G1470A / G1482A / G1500A / T1548C / C1557T / T1578C / C1605T / A1660G / C1764T / T1767C / G1791A / A1819T / T1899C",
    "AA_subs": "I61T / V63I / K262R / D272N / S405C / S409N / I554V / M607L",
    "t": 0.059,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0964,
    "dN": 0.0053,
    "dS": 0.0545,
    "N_x_dN": 8,
    "S_x_dS": 34.5
  },
  {
    "edge_num": 19,
    "subs": "G147T / T492C / A537G / T771C / A1128G / A1347G / T1497C / G1563A / C1620T / A1716G",
    "AA_subs": "",
    "t": 0.015,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0166,
    "N_x_dN": 0,
    "S_x_dS": 10.5
  },
  {
    "edge_num": 20,
    "subs": "G109T / A183T / A213G / G366A / C370A / A399G / C408T / G411A / A462G / G585A / G597A / T798C / T891C / G1009A / A1023G / C1062T / G1098A / A1134G / G1163A / T1167C / T1179C / T1305C / G1308A / C1338T / T1557C / G1572A / T1800C / T1819C / G2052A / G2145A",
    "AA_subs": "A37S / A337T / S388N",
    "t": 0.046,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0419,
    "dN": 0.002,
    "dS": 0.047,
    "N_x_dN": 3,
    "S_x_dS": 29.8
  },
  {
    "edge_num": 21,
    "subs": "C801T / A939G / A948G / G1026A / A1131G / A1267G / A1327C / G1344A / G1590A / C1686T / T1710C / G1869A / C1875T / C1893T / G2051A",
    "AA_subs": "I423V / G684E",
    "t": 0.024,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0549,
    "dN": 0.0013,
    "dS": 0.0237,
    "N_x_dN": 2,
    "S_x_dS": 15
  },
  {
    "edge_num": 22,
    "subs": "T183C / G210A / C420A / C1006A / G1116A / G1137A / C1221T / T1254C / C1410T / C1437T / C1993T",
    "AA_subs": "L336M",
    "t": 0.016,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0395,
    "dN": 0.0007,
    "dS": 0.0165,
    "N_x_dN": 1,
    "S_x_dS": 10.4
  },
  {
    "edge_num": 23,
    "subs": "T211C / T279C / G1134A / T1149C / C1179T / G1695T",
    "AA_subs": "",
    "t": 0.008,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0094,
    "N_x_dN": 0,
    "S_x_dS": 6
  },
  {
    "edge_num": 24,
    "subs": "",
    "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": "Sat Apr 13 06:03:31 2019"}
}
== testthat results  ===========================================================
OK: 125 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.65    0.21   11.07

Example timings

treeio.Rcheck/examples_i386/treeio-Ex.timings

nameusersystemelapsed
Nnode.treedata000
beast-mrbayes-parser0.110.000.12
drop.tip-methods0.010.000.02
getNodeNum0.020.000.01
read.astral000
read.codeml0.450.030.64
read.codeml_mlc0.050.000.05
read.hyphy0.010.000.17
read.hyphy.seq0.020.000.02
read.jplace0.030.000.06
read.nhx0.020.000.01
read.paml_rst0.370.000.50
read.phylip0.020.000.05
read.r8s0.000.000.06
read.raxml0.000.000.08
tree_subset000
write.beast0.030.000.10

treeio.Rcheck/examples_x64/treeio-Ex.timings

nameusersystemelapsed
Nnode.treedata000
beast-mrbayes-parser0.060.000.06
drop.tip-methods0.020.000.02
getNodeNum000
read.astral000
read.codeml0.250.000.25
read.codeml_mlc0.030.000.03
read.hyphy0.010.000.02
read.hyphy.seq0.020.000.01
read.jplace0.030.000.03
read.nhx000
read.paml_rst0.190.000.19
read.phylip0.010.000.02
read.r8s000
read.raxml0.020.000.01
tree_subset000
write.beast0.010.000.02