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BioC 3.4: CHECK report for ggtree on zin1

This page was generated on 2016-09-21 03:39:35 -0700 (Wed, 21 Sep 2016).

Package 515/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 1.5.14
Guangchuang Yu
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree
Last Changed Rev: 121115 / Revision: 121152
Last Changed Date: 2016-09-19 00:21:18 -0700 (Mon, 19 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]YES, new version is higher than in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: ggtree
Version: 1.5.14
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.5.14.tar.gz
StartedAt: 2016-09-20 07:18:15 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:19:07 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 51.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.5.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.5.14’
* 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 25.8Mb
  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 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-3.4-bioc/meat/ggtree.Rcheck/00check.log’
for details.


ggtree.Rcheck/00install.out:

* 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)

ggtree.Rcheck/ggtree-Ex.timings:

nameusersystemelapsed
NJ0.0000.0000.001
add-TREEDATA0.2080.0000.208
as.binary0.0120.0000.011
dotFun000
geom_tiplab0.1160.0000.118
get.fields-methods0.0080.0000.009
get.placements-methods0.0080.0000.008
get.subs-methods2.2920.0482.350
get.tree-methods0.0120.0000.011
get.treeinfo-methods0.0160.0000.014
get.treetext-methods0.0040.0000.005
ggtree0.1120.0000.109
gzoom.phylo0.3080.0000.607
plot-methods0.2920.0000.290
read.baseml0.9400.0080.947
read.beast0.0640.0000.065
read.codeml1.0720.0001.073
read.codeml_mlc0.040.000.04
read.hyphy0.0120.0000.011
read.jplace0.0080.0000.006
read.paml_rst0.6120.0000.621
show-methods0.0080.0000.007
theme_tree0.1080.0080.115
theme_tree20.1280.0000.130
update-TREE0.1280.0000.130
write.jplace0.0080.0000.007