BioC 3.5: CHECK report for treeio on malbec2

Package: treeio

Version: 1.0.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings treeio_1.0.2.tar.gz

StartedAt: 2017-10-18 02:58:25 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:59:07 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 41.7 seconds

RetCode: 0

Status:  OK

CheckDir: treeio.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings treeio_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/treeio.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.0.2’
* 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	0.084	0.000	0.086
Ntip	0.064	0.000	0.066
drop.tip-methods	0.140	0.000	0.137
get.fields-methods	0.064	0.000	0.064
get.placements-methods	0.096	0.000	0.098
get.subs-methods	2.244	0.016	2.263
get.tree-methods	0.020	0.000	0.023
get.treetext-methods	0.012	0.000	0.010
getNodeNum	0.000	0.000	0.001
getRoot	0	0	0
is.ggtree	0.472	0.004	0.489
read.baseml	0.968	0.004	0.973
read.beast	0.060	0.000	0.062
read.codeml	0.944	0.008	0.953
read.codeml_mlc	0.028	0.000	0.030
read.hyphy	0.008	0.000	0.010
read.jplace	0.012	0.000	0.010
read.nhx	0.008	0.000	0.008
read.paml_rst	0.544	0.000	0.544
read.phylip	0.008	0.000	0.008
read.r8s	0.020	0.000	0.016
read.raxml	0.008	0.000	0.008
show-methods	0.004	0.000	0.004
write.jplace	0.008	0.000	0.006