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BioC 3.5: CHECK report for treeio on malbec2

This page was generated on 2017-08-16 13:18:07 -0400 (Wed, 16 Aug 2017).

Package 1332/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treeio 1.0.2
Guangchuang Yu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/treeio
Last Changed Rev: 129299 / Revision: 131943
Last Changed Date: 2017-04-29 22:53:36 -0400 (Sat, 29 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: treeio
Version: 1.0.2
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings treeio_1.0.2.tar.gz
StartedAt: 2017-08-16 02:44:34 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:45:15 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 41.1 seconds
RetCode: 0
Status:  OK 
CheckDir: treeio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings treeio_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/treeio.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘treeio/DESCRIPTION’ ... OK
* this is package ‘treeio’ version ‘1.0.2’
* package encoding: UTF-8
* 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 ‘treeio’ can be installed ... OK
* checking installed package size ... OK
* 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: OK

treeio.Rcheck/00install.out:

* installing *source* package ‘treeio’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (treeio)

treeio.Rcheck/treeio-Ex.timings:

nameusersystemelapsed
Nnode0.0160.0040.017
Ntip0.0640.0040.066
drop.tip-methods0.1280.0000.130
get.fields-methods0.1200.0000.119
get.placements-methods0.0400.0040.041
get.subs-methods2.2280.0362.266
get.tree-methods0.0240.0000.025
get.treetext-methods0.0080.0000.005
getNodeNum0.0000.0000.001
getRoot0.0000.0000.001
is.ggtree0.4080.0000.431
read.baseml0.9720.0000.974
read.beast0.0600.0000.061
read.codeml0.9640.0000.964
read.codeml_mlc0.0280.0000.030
read.hyphy0.0120.0000.009
read.jplace0.0040.0000.005
read.nhx0.0080.0000.008
read.paml_rst0.5200.0000.521
read.phylip0.0040.0000.007
read.r8s0.0160.0000.017
read.raxml0.0080.0000.007
show-methods0.0000.0040.005
write.jplace0.0080.0000.006