BioC 3.2: CHECK report for ggtree on zin1

Package: ggtree

Version: 1.2.17

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.2.17.tar.gz

StartedAt: 2016-04-23 01:15:21 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:16:55 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 94.1 seconds

RetCode: 0

Status:  OK

CheckDir: ggtree.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.2.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ggtree.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.2.17’
* 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 ... [8s/8s] OK
* checking installed package size ... NOTE
  installed size is 21.9Mb
  sub-directories of 1Mb or more:
    doc       15.3Mb
    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 ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [3s/3s]
 [4s/4s] 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-3.2-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	0.000
add-TREEDATA	0.142	0.004	0.146
as.binary	0.015	0.000	0.015
dotFun	0.001	0.000	0.001
geom_tiplab	0.124	0.000	0.125
get.fields-methods	0.009	0.000	0.008
get.placements-methods	0.008	0.000	0.009
get.subs-methods	0.345	0.004	0.348
get.tree-methods	0.009	0.000	0.010
get.treeinfo-methods	0.016	0.000	0.016
get.treetext-methods	0.005	0.000	0.006
ggtree	0.109	0.000	0.109
gzoom.phylo	0.490	0.000	0.491
plot-methods	0.270	0.008	0.279
read.baseml	0.807	0.000	0.806
read.beast	0.060	0.004	0.063
read.codeml	0.900	0.004	0.903
read.codeml_mlc	0.037	0.000	0.038
read.hyphy	0.01	0.00	0.01
read.jplace	0.006	0.000	0.006
read.paml_rst	0.489	0.000	0.489
show-methods	0.006	0.000	0.006
theme_tree	0.11	0.00	0.11
theme_tree2	0.121	0.000	0.121
update-TREE	0.121	0.000	0.120
write.jplace	0.006	0.000	0.006