BioC 3.1: CHECK report for ggtree on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.0.21.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ggtree.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.21’
* 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 ... [7s/9s] OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc        5.6Mb
    examples   3.7Mb
    extdata    2.4Mb
* 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 ... [10s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/5s]
 [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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/ggtree.Rcheck/00check.log’
for details.

* installing *source* package ‘ggtree’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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	0.328	0.000	0.351
as.binary	0.016	0.000	0.015
dotFun	0.000	0.000	0.001
geom_tiplab	0.154	0.000	0.248
geom_tree	0.141	0.000	0.176
get.fields-methods	0.009	0.000	0.010
get.placements-methods	0.009	0.000	0.008
get.subs-methods	0.495	0.004	0.850
get.tree-methods	0.007	0.000	0.008
get.treeinfo-methods	0.019	0.000	0.040
get.treetext-methods	0.006	0.000	0.017
ggtree	0.123	0.004	0.197
gplot	0.310	0.000	0.514
gzoom.phylo	0.538	0.000	0.730
plot-methods	0.324	0.003	0.329
read.baseml	1.415	0.000	2.615
read.beast	0.076	0.000	0.166
read.codeml	1.517	0.000	2.063
read.codeml_mlc	0.048	0.000	0.092
read.hyphy	0.008	0.000	0.008
read.jplace	0.010	0.000	0.025
read.paml_rst	0.946	0.000	1.353
show-methods	0.006	0.000	0.005
theme_tree	0.133	0.000	0.180
theme_tree2	0.129	0.007	0.136
update.TREE	0.167	0.000	0.181
write.jplace	0.007	0.000	0.006

BioC 3.1: CHECK report for ggtree on zin2

Summary

Command output