BioC 3.3: CHECK report for ggtree on morelia

Package: ggtree

Version: 1.3.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.3.15.tar.gz

StartedAt: 2016-04-21 03:13:39 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 03:16:09 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 149.8 seconds

RetCode: 0

Status:  OK

CheckDir: ggtree.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.3.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ggtree.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.3.15’
* 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 ... [11s/13s] OK
* checking installed package size ... NOTE
  installed size is 32.1Mb
  sub-directories of 1Mb or more:
    doc       25.4Mb
    examples   3.7Mb
    extdata    2.5Mb
* 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 ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [5s/5s]
 [5s/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-3.3-bioc/meat/ggtree.Rcheck/00check.log’
for details.

* installing *source* package ‘ggtree’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggtree)

name	user	system	elapsed
NJ	0.001	0.000	0.001
add-TREEDATA	0.268	0.003	0.284
as.binary	0.019	0.000	0.020
dotFun	0.001	0.001	0.001
geom_tiplab	0.212	0.001	0.214
get.fields-methods	0.015	0.001	0.016
get.placements-methods	0.016	0.000	0.016
get.subs-methods	0.519	0.005	0.532
get.tree-methods	0.021	0.000	0.022
get.treeinfo-methods	0.021	0.001	0.022
get.treetext-methods	0.016	0.000	0.017
ggtree	0.196	0.001	0.197
gzoom.phylo	0.570	0.009	0.600
plot-methods	0.499	0.002	0.507
read.baseml	1.703	0.008	1.764
read.beast	0.105	0.001	0.106
read.codeml	1.791	0.015	1.833
read.codeml_mlc	0.095	0.001	0.098
read.hyphy	0.020	0.001	0.021
read.jplace	0.013	0.000	0.013
read.paml_rst	1.008	0.008	1.025
show-methods	0.015	0.001	0.016
theme_tree	0.182	0.001	0.186
theme_tree2	0.215	0.006	0.226
update-TREE	0.208	0.002	0.213
write.jplace	0.010	0.000	0.011