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phylobase log file (check_x86_64_linux)

Thu May  8 18:17:23 2014: Checking package phylobase (SVN revision 951) ...
* using log directory ‘/mnt/building/build_2014-05-08-18-10/RF_PKG_CHECK/PKGS/phylobase.Rcheck’
* using R version 3.1.0 Patched (2014-05-07 r65539)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘phylobase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phylobase’ version ‘0.6.9-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Francois Michonneau ’
Unknown, possibly mis-spelled, fields in DESCRIPTION:
  ‘Roxygen’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phylobase’ can be installed ... [114s/120s] OK
* checking installed package size ... NOTE
  installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
* 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 line widths ... NOTE
Rd file 'phylomat-class.Rd':
  \examples lines wider than 100 characters:
     tree.owls <- ape::read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")

Rd file 'setAs-methods.Rd':
  \examples lines wider than 100 characters:
     tree.owls <- ape::read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")

These lines will be truncated in the PDF manual.
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’
  Running ‘misctests.R’
  Comparing ‘misctests.Rout’ to ‘misctests.Rout.save’ ... OK
  Running ‘phylo4dtests.R’
  Comparing ‘phylo4dtests.Rout’ to ‘phylo4dtests.Rout.save’ ... OK
  Running ‘phylosubtest.R’
  Comparing ‘phylosubtest.Rout’ to ‘phylosubtest.Rout.save’ ... OK
  Running ‘phylotorture.R’
  Comparing ‘phylotorture.Rout’ to ‘phylotorture.Rout.save’ ...34,36d33
< Error in .local(x, ...) : Tree is reticulated.
< Error in names(res) <- switch(type, tip = 1:ntips, internal = seq(from = ntips +  : 
<   'names' attribute [2] must be the same length as the vector [1]
38a36,38
> Error in names(res) <- switch(type, tip = 1:ntips, internal = seq(from = ntips +  : 
>   'names' attribute [2] must be the same length as the vector [1]
> Error in .local(x, ...) : Nodes incorrectly labeled. 
41c41
< [1]  13  44 143
---
> [1]  3 44 53
42a43
> There are 100 valid trees...
65a67,69
> number of trees with polytomies: 100
> number of trees with singletons: 0
> number of trees with reticulation: 100
89,90c93,96
< Warning message:
< In checkTree(object) : Tree contains singleton nodes. 
---
> Warning messages:
> 1: In checkTree(object) : Tree contains singleton nodes. 
> 2: In checkTree(object) : Tree contains singleton nodes. 
> 3: In checkTree(object) : Tree contains singleton nodes. 
  Running ‘plottest.R’
  Comparing ‘plottest.Rout’ to ‘plottest.Rout.save’ ... OK
  Running ‘roundtrip.R’
  Comparing ‘roundtrip.Rout’ to ‘roundtrip.Rout.save’ ... OK
  Running ‘test-all.R’
  Running ‘testprune.R’
  Comparing ‘testprune.Rout’ to ‘testprune.Rout.save’ ... OK
 [19s/19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘developer.Rnw’ using ‘UTF-8’ ... [0s/0s] OK
   ‘phylobase.Rnw’ using ‘UTF-8’ ... [2s/2s] OK
 [3s/3s] OK
* checking re-building of vignette outputs ... [4s/5s] OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/mnt/building/build_2014-05-08-18-10/RF_PKG_CHECK/PKGS/phylobase.Rcheck/00check.log’
for details.

Run time: 220.02 seconds.