• using R version 2.15.3 (2013-03-01)
• using platform: i386-w64-mingw32 (32-bit)
• using session charset: ISO8859-1
• checking for file 'phylobase/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'phylobase' version '0.6.5.2'
• 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 whether package 'phylobase' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... 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
  ** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
• checking for unstated 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 contents of 'data' directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... 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' OK
  Running 'RUnit-tests.R'
  Comparing 'RUnit-tests.Rout' to 'RUnit-tests.Rout.save' ... OK
  Running 'doRUnit.R'
  Running 'misctests.R'
  Comparing 'misctests.Rout' to 'misctests.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'nexusdata.R'
  Comparing 'nexusdata.Rout' to 'nexusdata.Rout.save' ... OK
  Running 'phylo4dtests.R'
  Comparing 'phylo4dtests.Rout' to 'phylo4dtests.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'phylosubtest.R'
  Comparing 'phylosubtest.Rout' to 'phylosubtest.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'phylotorture.R'
  Comparing 'phylotorture.Rout' to 'phylotorture.Rout.save' ...8c8
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'plottest.R'
  Comparing 'plottest.Rout' to 'plottest.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'roundtrip.R'
  Comparing 'roundtrip.Rout' to 'roundtrip.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'testprune.R'
  Comparing 'testprune.Rout' to 'testprune.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  ** running tests for arch 'x64' OK
  Running 'RUnit-tests.R'
  Comparing 'RUnit-tests.Rout' to 'RUnit-tests.Rout.save' ... OK
  Running 'doRUnit.R'
  Running 'misctests.R'
  Comparing 'misctests.Rout' to 'misctests.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'nexusdata.R'
  Comparing 'nexusdata.Rout' to 'nexusdata.Rout.save' ... OK
  Running 'phylo4dtests.R'
  Comparing 'phylo4dtests.Rout' to 'phylo4dtests.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'phylosubtest.R'
  Comparing 'phylosubtest.Rout' to 'phylosubtest.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'phylotorture.R'
  Comparing 'phylotorture.Rout' to 'phylotorture.Rout.save' ...8c8
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'plottest.R'
  Comparing 'plottest.Rout' to 'plottest.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'roundtrip.R'
  Comparing 'roundtrip.Rout' to 'roundtrip.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
  Running 'testprune.R'
  Comparing 'testprune.Rout' to 'testprune.Rout.save' ...7c7
  < The following object(s) are masked from 'package:ape':
  ---
  > The following object is masked from 'package:ape':
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... OK
• checking PDF version of manual ... OK