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BioC 3.2: CHECK report for ggtree on zin1

This page was generated on 2015-08-24 10:50:23 -0700 (Mon, 24 Aug 2015).

Package 428/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 1.1.16
Guangchuang Yu
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree
Last Changed Rev: 107527 / Revision: 107696
Last Changed Date: 2015-08-17 23:47:24 -0700 (Mon, 17 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.1.16
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.1.16.tar.gz
StartedAt: 2015-08-24 00:20:44 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:22:53 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 129.2 seconds
RetCode: 0
Status:  OK 
CheckDir: ggtree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ggtree_1.1.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ggtree.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.1.16’
* 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/11s] OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    examples   3.7Mb
    extdata    2.0Mb
* 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
  ‘/home/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
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Creating a new generic function for ‘reroot’ in package ‘ggtree’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘jsonlite’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (ggtree)

ggtree.Rcheck/ggtree-Ex.timings:

nameusersystemelapsed
NJ0.0010.0000.001
add.TREEDATA0.2230.0120.236
as.binary0.020.000.02
dotFun0.0000.0000.001
geom_aline0.220.000.22
geom_tiplab0.3660.0000.367
geom_tippoint0.1540.0080.163
geom_tree0.1660.0040.169
get.fields-methods0.010.000.01
get.placements-methods0.0090.0000.009
get.subs-methods0.5430.0000.543
get.tree-methods0.0080.0000.009
get.treeinfo-methods0.0190.0040.022
get.treetext-methods0.0060.0000.006
ggtree0.1350.0000.136
gplot0.3390.0040.367
gzoom.phylo0.5410.0080.573
plot-methods0.3390.0000.340
read.baseml1.5510.0001.566
read.beast0.0730.0000.073
read.codeml1.5170.0001.516
read.codeml_mlc0.0430.0000.046
read.hyphy0.0080.0000.009
read.jplace0.0060.0000.005
read.paml_rst0.8770.0000.897
show-methods0.0070.0000.006
theme_tree0.1490.0000.149
theme_tree20.1450.0000.144
update.TREE0.1840.0000.183
write.jplace0.0070.0000.006