BioC 3.2: CHECK report for ggtree on perceval

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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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [19s/19s] OK
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc        3.4Mb
    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 ... [16s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [7s/7s]
 [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	0.001	0.000	0.001
add.TREEDATA	0.215	0.003	0.218
as.binary	0.042	0.001	0.043
dotFun	0.001	0.000	0.001
geom_aline	0.243	0.001	0.244
geom_tiplab	0.218	0.002	0.219
geom_tippoint	0.206	0.002	0.208
geom_tree	0.233	0.002	0.235
get.fields-methods	0.012	0.000	0.036
get.placements-methods	0.011	0.000	0.011
get.subs-methods	0.596	0.009	0.605
get.tree-methods	0.011	0.001	0.012
get.treeinfo-methods	0.030	0.002	0.031
get.treetext-methods	0.008	0.001	0.009
ggtree	0.190	0.002	0.192
gplot	0.418	0.003	0.421
gzoom.phylo	0.795	0.006	0.811
plot-methods	0.407	0.002	0.410
read.baseml	1.547	0.006	1.553
read.beast	0.093	0.001	0.095
read.codeml	1.707	0.009	1.717
read.codeml_mlc	0.058	0.000	0.059
read.hyphy	0.01	0.00	0.01
read.jplace	0.015	0.001	0.015
read.paml_rst	0.880	0.004	0.884
show-methods	0.02	0.00	0.02
theme_tree	0.189	0.002	0.190
theme_tree2	0.203	0.001	0.205
update.TREE	0.250	0.002	0.253
write.jplace	0.009	0.001	0.009

BioC 3.2: CHECK report for ggtree on perceval

Summary

Command output