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BioC 3.2: CHECK report for ggtree on oaxaca

This page was generated on 2016-04-23 10:28:50 -0700 (Sat, 23 Apr 2016).

Package 440/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 1.2.17
Guangchuang Yu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ggtree
Last Changed Rev: 114635 / Revision: 116712
Last Changed Date: 2016-03-10 22:37:59 -0800 (Thu, 10 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ggtree
Version: 1.2.17
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.2.17.tar.gz
StartedAt: 2016-04-23 00:41:08 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:43:43 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 154.9 seconds
RetCode: 0
Status:  OK 
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.2.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ggtree.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.2.17’
* 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 ... [10s/16s] OK
* checking installed package size ... NOTE
  installed size is 32.0Mb
  sub-directories of 1Mb or more:
    doc       25.4Mb
    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 ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [4s/4s]
 [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-3.2-bioc/meat/ggtree.Rcheck/00check.log’
for details.


ggtree.Rcheck/00install.out:

* 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)

ggtree.Rcheck/ggtree-Ex.timings:

nameusersystemelapsed
NJ0.0010.0000.000
add-TREEDATA0.1850.0020.199
as.binary0.0240.0010.024
dotFun000
geom_tiplab0.1580.0010.159
get.fields-methods0.0120.0010.047
get.placements-methods0.0120.0000.012
get.subs-methods0.5090.0030.512
get.tree-methods0.0190.0000.019
get.treeinfo-methods0.0210.0010.023
get.treetext-methods0.0040.0010.004
ggtree0.1120.0010.113
gzoom.phylo0.6080.0090.643
plot-methods0.4100.0120.422
read.baseml1.1340.0141.148
read.beast0.0790.0000.079
read.codeml1.4700.0121.483
read.codeml_mlc0.0840.0000.085
read.hyphy0.0130.0010.013
read.jplace0.0050.0000.005
read.paml_rst0.8780.0040.882
show-methods0.0130.0010.013
theme_tree0.1620.0010.164
theme_tree20.1760.0030.181
update-TREE0.1660.0020.232
write.jplace0.0070.0000.009