• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘vegan/DESCRIPTION’ ... OK
• this is package ‘vegan’ version ‘2.0-4’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking whether package ‘vegan’ 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
• 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 ... WARNING
  Foreign function call(s) with ‘PACKAGE’ argument in a base package:
  .C("dblcen", ..., PACKAGE = "stats")
  Foreign function call(s) with ‘PACKAGE’ argument in different package:
  .C("count", ..., PACKAGE = "cclust")
  Undeclared package(s) in foreign function calls
  ‘cclust’
  See the chapter ‘System and foreign language interfaces’ of the
  ‘Writing R Extensions’ manual.
• 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 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 ... [52s/52s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [9s/9s] OK
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  ABD: EverySelectfont initializing macros)) (./intro-vegan.toc)
  (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1fi4.fd) [1{/var/lib/texm
  f/fonts/map/pdftex/updmap/pdftex.map}]
  (/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
  
  LaTeX Font Warning: Font shape `T1/fi4/m/sl' undefined
  (Font) using `T1/fi4/m/n' instead on input line 80.
  
  
  Overfull \hbox (5.47499pt too wide) has occurred while \output is active
  \T1/aer/m/n/10.95 2 []
  [2
  ./intro-vegan.tex:126: pdfTeX error (ext4): \pdfendlink ended up in different n
  esting level than \pdfstartlink.
  \AtBegShi@Output ...ipout \box \AtBeginShipoutBox
  \fi \fi
  l.126 \begin{Sinput}
  
  ./intro-vegan.tex:126: ==> Fatal error occurred, no output PDF file produced!
  Transcript written on intro-vegan.log.
  /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
  make: *** [intro-vegan.pdf] Error 1
  Error in buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel/Work/PKGS/vegan.Rcheck/vign_test/vegan") :
  running 'make' failed
  Execution halted
  
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There was 1 note.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/vegan.Rcheck/00check.log’
  for details.