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BioC 3.2: CHECK report for ggtree on perceval

This page was generated on 2015-10-26 18:17:26 -0400 (Mon, 26 Oct 2015).

Package 440/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggtree 1.2.1
Guangchuang Yu
Snapshot Date: 2015-10-25 19:24:07 -0400 (Sun, 25 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ggtree
Last Changed Rev: 109786 / Revision: 109913
Last Changed Date: 2015-10-20 06:28:56 -0400 (Tue, 20 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK YES, new version is higher than 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: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggtree_1.2.1.tar.gz
StartedAt: 2015-10-26 09:34:40 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 09:36:58 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 138.4 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ggtree.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.1’
* 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/12s] OK
* checking installed package size ... NOTE
  installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    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 ... [14s/14s] 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
  ‘/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
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.
** 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
NJ0.0000.0000.001
add.TREEDATA0.4270.0180.444
as.binary0.0390.0000.040
dotFun0.0010.0000.001
geom_tiplab0.2130.0010.215
geom_tree0.2200.0020.222
get.fields-methods0.0110.0010.025
get.placements-methods0.0130.0010.014
get.subs-methods0.6220.0050.628
get.tree-methods0.0110.0000.012
get.treeinfo-methods0.0280.0010.030
get.treetext-methods0.0080.0000.008
ggtree0.2020.0010.204
gplot0.3950.0020.397
gzoom.phylo0.7300.0030.747
plot-methods0.4180.0010.421
read.baseml1.9010.0071.908
read.beast0.0980.0000.098
read.codeml1.8400.0041.845
read.codeml_mlc0.0630.0010.064
read.hyphy0.0120.0010.012
read.jplace0.0070.0000.007
read.paml_rst0.9730.0030.975
show-methods0.0070.0010.007
theme_tree0.1830.0050.189
theme_tree20.1960.0020.199
update.TREE0.2400.0090.249
write.jplace0.0080.0010.009