• 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 ‘adephylo/DESCRIPTION’ ... OK
• this is package ‘adephylo’ version ‘1.1-2’
• 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 for executable files ... OK
• checking for hidden files and directories ... OK
• checking whether package ‘adephylo’ 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 ... NOTE
  Foreign function call(s) with ‘PACKAGE’ argument in different package:
  .C("VarianceDecompInOrthoBasis", ..., PACKAGE = "ade4")
  See the chapter ‘System and foreign language interfaces’ of the
  ‘Writing R Extensions’ manual.
• checking R code for possible problems ... NOTE
  abouheif.moran: warning in matrix(res$result, ncol = nvar, byr = TRUE):
  partial argument match of 'byr' to 'byrow'
  orthogram: warning in arrows(mp[x0], sig50[x0], mp[x0], phylocum[x0],
  ang = 15, le = 0.15, lwd = 2): partial argument match of 'le' to
  'length'
  orthogram: warning in arrows(mp[x0], sig50[x0], mp[x0], phylocum[x0],
  ang = 15, le = 0.15, lwd = 2): partial argument match of 'ang' to
  'angle'
  plot.ppca: warning in dotchart(x$c1[, 1], lab = row.names(x$c1), main =
  "Loadings", cex = par("cex") * 0.66): partial argument match of 'lab'
  to 'labels'
  ppca: warning in eigen(((t(X) %*% W %*% X)/N), sym = TRUE): partial
  argument match of 'sym' to 'symmetric'
  sp.tips : pathTwoTips: warning in factor(cpath, level = unique(cpath)):
  partial argument match of 'level' to 'levels'
• 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 ... NOTE
  File ‘/home/hornik/tmp/R.check/r-devel/Work/build/Packages/adephylo/libs/adephylo.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
  Object: ‘distPhylo.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Object: ‘distPhylo.o’
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following directories should probably not be installed:
  ‘figs’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [18s/18s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [3s/3s] OK
• checking re-building of vignette PDFs ... [6s/6s] OK
• checking PDF version of manual ... OK
  NOTE: There were 4 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/adephylo.Rcheck/00check.log’
  for details.