• using R version 2.14.0 (2011-10-31)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'phangorn/DESCRIPTION' ... OK
• this is package 'phangorn' version '1.5-1'
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: 'seqLogo'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'phangorn' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level 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 'x86_64'
  ** 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 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 R/sysdata.rda ... 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 examples ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x86_64' ... OK
• 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 ... NOTE
  Error in re-building vignettes:
  ...
  Loading required package: igraph
  Loading required package: Matrix
  Loading required package: lattice
  
  Attaching package: 'Matrix'
  
  The following object(s) are masked from 'package:base':
  
  det
  
  Loading required package: seqLogo
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'seqLogo'
  Loading required package: seqLogo
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'seqLogo'
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
  Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
  Running 'texi2dvi' on 'Ancestral.tex' failed.
  LaTeX errors:
  !pdfTeX error: pdflatex (file ./Ancestral-figLOGO.pdf): PDF inclusion: required
  page does not exist <0>
  ==> Fatal error occurred, no output PDF file produced!
  Calls: buildVignettes -> texi2pdf -> texi2dvi
  Execution halted
  
• checking PDF version of manual ... OK
• elapsed time (check, wall clock): 4:38