BioC 3.3: CHECK report for ggtree on zin2

Package: ggtree

Version: 1.4.20

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.4.20.tar.gz

StartedAt: 2016-10-13 02:40:48 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:41:49 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 60.6 seconds

RetCode: 0

Status:  OK

CheckDir: ggtree.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.4.20.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ggtree.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.4.20’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 25.7Mb
  sub-directories of 1Mb or more:
    doc       18.8Mb
    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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.3-bioc/meat/ggtree.Rcheck/00check.log’
for details.

* installing *source* package ‘ggtree’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
Note: wrong number of arguments to '>' 
** 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	0.225	0.007	0.234
as.binary	0.014	0.001	0.013
dotFun	0.001	0.000	0.000
geom_tiplab	0.146	0.000	0.146
get.fields-methods	0.012	0.000	0.012
get.placements-methods	0.005	0.000	0.009
get.subs-methods	2.606	0.037	2.657
get.tree-methods	0.009	0.004	0.013
get.treeinfo-methods	0.015	0.000	0.015
get.treetext-methods	0.006	0.000	0.006
ggtree	0.122	0.000	0.122
gzoom.phylo	0.360	0.000	0.372
plot-methods	0.330	0.000	0.338
read.baseml	1.056	0.004	1.060
read.beast	0.082	0.000	0.083
read.codeml	1.186	0.000	1.199
read.codeml_mlc	0.045	0.000	0.046
read.hyphy	0.012	0.000	0.013
read.jplace	0.007	0.000	0.006
read.paml_rst	0.669	0.003	0.685
show-methods	0.012	0.000	0.012
theme_tree	0.134	0.000	0.133
theme_tree2	0.144	0.000	0.143
update-TREE	0.147	0.000	0.146
write.jplace	0.006	0.000	0.007