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BioC 3.5: CHECK report for treeio on tokay2

This page was generated on 2017-08-16 13:26:32 -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: rm -rf treeio.buildbin-libdir treeio.Rcheck && mkdir treeio.buildbin-libdir treeio.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=treeio.buildbin-libdir treeio_1.0.2.tar.gz >treeio.Rcheck\00install.out 2>&1 && cp treeio.Rcheck\00install.out treeio-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=treeio.buildbin-libdir --install="check:treeio-install.out" --force-multiarch --no-vignettes --timings treeio_1.0.2.tar.gz
StartedAt: 2017-08-16 03:21:07 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:22:28 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 81.2 seconds
RetCode: 0
Status:  OK  
CheckDir: treeio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf treeio.buildbin-libdir treeio.Rcheck && mkdir treeio.buildbin-libdir treeio.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=treeio.buildbin-libdir treeio_1.0.2.tar.gz >treeio.Rcheck\00install.out 2>&1 && cp treeio.Rcheck\00install.out treeio-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=treeio.buildbin-libdir --install="check:treeio-install.out" --force-multiarch --no-vignettes --timings treeio_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/treeio.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:


install for i386

* 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

install for x64

* installing *source* package 'treeio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'treeio' as treeio_1.0.2.zip
* DONE (treeio)

treeio.Rcheck/examples_i386/treeio-Ex.timings:

nameusersystemelapsed
Nnode0.030.000.03
Ntip0.110.000.11
drop.tip-methods0.220.000.22
get.fields-methods0.080.000.08
get.placements-methods0.040.000.05
get.subs-methods2.280.102.37
get.tree-methods0.050.000.05
get.treetext-methods000
getNodeNum0.010.000.01
getRoot000
is.ggtree0.240.000.24
read.baseml0.920.010.93
read.beast0.050.000.13
read.codeml1.430.051.48
read.codeml_mlc0.050.000.05
read.hyphy0.020.000.01
read.jplace0.000.020.02
read.nhx0.010.000.02
read.paml_rst0.550.040.59
read.phylip000
read.r8s0.030.000.03
read.raxml000
show-methods0.020.000.02
write.jplace000

treeio.Rcheck/examples_x64/treeio-Ex.timings:

nameusersystemelapsed
Nnode0.040.000.03
Ntip0.070.000.08
drop.tip-methods0.140.000.14
get.fields-methods0.090.000.09
get.placements-methods0.050.000.05
get.subs-methods2.780.062.85
get.tree-methods0.020.000.02
get.treetext-methods000
getNodeNum000
getRoot000
is.ggtree0.490.000.49
read.baseml0.950.051.00
read.beast0.100.000.16
read.codeml0.980.011.00
read.codeml_mlc0.030.000.03
read.hyphy0.010.000.02
read.jplace000
read.nhx0.020.000.01
read.paml_rst0.580.020.60
read.phylip0.010.000.01
read.r8s0.030.000.03
read.raxml0.020.000.02
show-methods0.010.000.02
write.jplace0.020.000.01