BioC 3.2: CHECK report for ggtree on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.1.16.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ggtree.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggtree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggtree’ version ‘1.1.16’
* 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 ‘ggtree’ can be installed ... [16s/18s] OK
* checking installed package size ... NOTE
  installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   3.7Mb
    extdata    2.0Mb
* 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 loading without being on the library search path ... 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 ... [18s/21s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [7s/8s]
 [8s/8s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ggtree.Rcheck/00check.log’
for details.

* installing *source* package ‘ggtree’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Creating a new generic function for ‘reroot’ in package ‘ggtree’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (ggtree)

name	user	system	elapsed
NJ	0.000	0.000	0.003
add.TREEDATA	0.277	0.011	0.332
as.binary	0.027	0.002	0.033
dotFun	0.001	0.000	0.000
geom_aline	0.545	0.005	0.595
geom_tiplab	0.218	0.008	0.249
geom_tippoint	0.224	0.018	0.269
geom_tree	0.217	0.003	0.242
get.fields-methods	0.013	0.001	0.039
get.placements-methods	0.012	0.000	0.013
get.subs-methods	0.726	0.009	0.805
get.tree-methods	0.016	0.001	0.017
get.treeinfo-methods	0.025	0.001	0.048
get.treetext-methods	0.007	0.000	0.007
ggtree	0.177	0.001	0.189
gplot	0.466	0.001	0.519
gzoom.phylo	0.771	0.018	0.879
plot-methods	0.491	0.002	0.548
read.baseml	2.153	0.013	2.265
read.beast	0.118	0.000	0.120
read.codeml	2.476	0.010	2.630
read.codeml_mlc	0.114	0.001	0.125
read.hyphy	0.017	0.001	0.022
read.jplace	0.008	0.001	0.009
read.paml_rst	1.430	0.005	1.623
show-methods	0.008	0.001	0.009
theme_tree	0.193	0.001	0.222
theme_tree2	0.207	0.001	0.231
update.TREE	0.249	0.001	0.286
write.jplace	0.009	0.002	0.014

BioC 3.2: CHECK report for ggtree on oaxaca

Summary

Command output