BioC 3.5: CHECK report for treeio on veracruz2

Package: treeio

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings treeio_1.0.2.tar.gz

StartedAt: 2017-10-18 09:52:11 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:53:01 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 49.9 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_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/treeio.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.0.2’
* 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)

name	user	system	elapsed
Nnode	0.072	0.001	0.074
Ntip	0.088	0.004	0.095
drop.tip-methods	0.177	0.001	0.183
get.fields-methods	0.092	0.001	0.095
get.placements-methods	0.055	0.001	0.058
get.subs-methods	2.662	0.076	2.813
get.tree-methods	0.032	0.001	0.034
get.treetext-methods	0.005	0.000	0.006
getNodeNum	0.001	0.000	0.001
getRoot	0.001	0.000	0.001
is.ggtree	0.516	0.017	0.545
read.baseml	1.084	0.017	1.136
read.beast	0.083	0.001	0.089
read.codeml	1.318	0.014	1.364
read.codeml_mlc	0.054	0.001	0.056
read.hyphy	0.018	0.001	0.018
read.jplace	0.006	0.000	0.006
read.nhx	0.009	0.000	0.009
read.paml_rst	0.809	0.011	0.854
read.phylip	0.011	0.000	0.012
read.r8s	0.027	0.000	0.028
read.raxml	0.011	0.001	0.013
show-methods	0.006	0.000	0.006
write.jplace	0.008	0.001	0.009