• using R version 2.15.0 (2012-03-30)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘picante/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘picante’ version ‘1.3-0’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for executable files ... OK
• checking whether package ‘picante’ 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 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 ... NOTE
  Kcalc: warning in vcv.phylo(phy, cor = TRUE): partial argument match of
  'cor' to 'corr'
  pblm: warning in vcv.phylo(tree1, cor = TRUE): partial argument match
  of 'cor' to 'corr'
  pblm: warning in vcv.phylo(tree2, cor = TRUE): partial argument match
  of 'cor' to 'corr'
  pblmpredict: warning in vcv.phylo(tree1.w.novel, cor = TRUE): partial
  argument match of 'cor' to 'corr'
  pblmpredict: warning in vcv.phylo(tree2.w.novel, cor = TRUE): partial
  argument match of 'cor' to 'corr'
  pcd: warning in vcv.phylo(tree, cor = TRUE): partial argument match of
  'cor' to 'corr'
  phylostruct: warning in randomizeMatrix(samp, null.model = null.model,
  it = it): partial argument match of 'it' to 'iterations'
  psc: warning in vcv.phylo(tree, cor = TRUE): partial argument match of
  'cor' to 'corr'
  pse: warning in vcv.phylo(tree, cor = TRUE): partial argument match of
  'cor' to 'corr'
  psv: warning in vcv.phylo(tree, cor = TRUE): partial argument match of
  'cor' to 'corr'
  psv.spp: warning in vcv.phylo(tree, cor = TRUE): partial argument match
  of 'cor' to 'corr'
  sppregs: warning in vcv.phylo(tree, cor = TRUE): partial argument match
  of 'cor' to 'corr'
• 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 ... [45s/45s] OK
• checking for unstated dependencies in vignettes ... NOTE
  ‘library’ or ‘require’ call not declared from: ‘cluster’
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [1s/1s] WARNING
  Errors in running code in vignettes:
  when running code in ‘picante-intro.Rnw’
  ...
  clump2b 7.12500 7.62500
  clump4 8.06250 7.62500 7.62500
  even 8.06250 8.06250 8.06250 7.87500
  random 7.81250 7.68750 7.93750 8.12500 8.03125
  
  > library(cluster)
  
  When sourcing ‘picante-intro.R’:
  Error: there is no package called ‘cluster’
  Execution halted
  
• checking re-building of vignette PDFs ... [4s/4s] OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 3 notes.
  See
  ‘/home/hornik/tmp/R.check/r-release/Work/PKGS/picante.Rcheck/00check.log’
  for details.