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_1.2.2.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 ‘1.2.2’
* 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 ... [10s/19s] OK
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   3.7Mb
    extdata    2.3Mb
* 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 ... [14s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [4s/4s]
 [4s/5s] 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.
** 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	0.001	0.000	0.001
add.TREEDATA	0.394	0.015	0.408
as.binary	0.024	0.000	0.024
dotFun	0.001	0.000	0.001
geom_tiplab	0.202	0.001	0.203
geom_tree	0.209	0.002	0.211
get.fields-methods	0.013	0.001	0.033
get.placements-methods	0.015	0.000	0.015
get.subs-methods	0.735	0.007	0.742
get.tree-methods	0.016	0.000	0.016
get.treeinfo-methods	0.030	0.000	0.031
get.treetext-methods	0.008	0.000	0.008
ggtree	0.193	0.001	0.194
gplot	0.419	0.002	0.422
gzoom.phylo	0.773	0.009	0.797
plot-methods	0.434	0.001	0.436
read.baseml	2.180	0.011	2.192
read.beast	0.099	0.001	0.099
read.codeml	2.187	0.010	2.198
read.codeml_mlc	0.087	0.001	0.089
read.hyphy	0.013	0.001	0.014
read.jplace	0.005	0.000	0.005
read.paml_rst	0.945	0.007	0.951
show-methods	0.005	0.000	0.005
theme_tree	0.182	0.004	0.186
theme_tree2	0.155	0.009	0.164
update.TREE	0.181	0.002	0.184
write.jplace	0.005	0.000	0.006

BioC 3.2: CHECK report for ggtree on oaxaca

Summary

Command output