Package: treeio

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings treeio_1.2.2.tar.gz

StartedAt: 2018-04-12 10:29:10 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:30:08 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 57.7 seconds

RetCode: 0

Status:  OK

CheckDir: treeio.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings treeio_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/treeio.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘treeio/DESCRIPTION’ ... OK
* this is package ‘treeio’ version ‘1.2.2’
* 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 installed files from ‘inst/doc’ ... 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

* installing *source* package ‘treeio’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (treeio)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  5.035   0.106   5.220 

name	user	system	elapsed
Nnode	0.025	0.002	0.028
Ntip	0.087	0.001	0.088
drop.tip-methods	0.170	0.002	0.176
get.fields-methods	0.080	0.001	0.083
get.placements-methods	0.051	0.000	0.052
get.subs-methods	2.771	0.073	2.893
get.tree-methods	0.037	0.001	0.038
get.treetext-methods	0.005	0.000	0.006
getNodeNum	0.002	0.000	0.002
getRoot	0.001	0.000	0.001
is.ggtree	0.498	0.015	0.527
read.baseml	1.104	0.015	1.130
read.beast	0.084	0.001	0.087
read.codeml	1.299	0.011	1.340
read.codeml_mlc	0.057	0.000	0.062
read.hyphy	0.017	0.000	0.018
read.jplace	0.005	0.001	0.007
read.nhx	0.009	0.000	0.010
read.paml_rst	0.759	0.008	0.789
read.phylip	0.011	0.001	0.011
read.r8s	0.013	0.000	0.012
read.raxml	0.006	0.000	0.006
show-methods	0.006	0.000	0.006
write.jplace	0.006	0.001	0.007