• using R version 2.11.0 Under development (unstable) (2009-10-31 r50269)
• using session charset: UTF-8
• checking for file 'ade4/DESCRIPTION' ... OK
• this is package 'ade4' version '1.4-11'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking for executable files ... OK
• checking whether package 'ade4' can be installed ... 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 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
  hclust2phylog: possible error in gsub(paste(labels.nodes[j], ":", sep =
  ""), w, tre, ext = FALSE): unused argument(s) (ext = FALSE)
  kdisteuclid : selectinlist.util: possible error in regexpr(w, ref, ext
  = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in gsub("\\[[^\\[]*\\]", "",
  x.tre, ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in gsub(" ", "", x.tre, ext =
  FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in gsub("[.]", "_", leurre,
  ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in sub(old, leurre[i], x.tre,
  ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete : label: possible error in gsub("[.]", "_",
  lab, ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in gsub("[.]", "_", labels,
  ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in sub(leurre[i], new, x.tre,
  ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in regexpr(paste(")", new, sep
  = ""), x.tre, ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in regexpr(paste(",", new, sep
  = ""), x.tre, ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog : complete: possible error in regexpr(paste("(", new, sep
  = ""), x.tre, ext = FALSE): unused argument(s) (ext = FALSE)
  newick2phylog: possible error in regexpr("([^()]*)", x.tre, ext =
  FALSE): unused argument(s) (ext = FALSE)
  newick2phylog: possible error in strsplit(x.tre, chaavec, ext = FALSE):
  unused argument(s) (ext = FALSE)
  newick2phylog: possible error in strsplit(w1, "[,);]", ext = FALSE):
  unused argument(s) (ext = FALSE)
  newick2phylog: possible error in gsub(chaavec, "", x.tre, ext = FALSE):
  unused argument(s) (ext = FALSE)
  phylog.permut : adddistances: possible error in
  sub(paste(leaves.names[i], ",", sep = ""), paste(leaves.names[i],
  ":", phylog$leaves[i], ",", sep = ""), tre, extended = FALSE): unused
  argument(s) (extended = FALSE)
  phylog.permut : adddistances: possible error in
  sub(paste(leaves.names[i], ")", sep = ""), paste(leaves.names[i],
  ":", phylog$leaves[i], ")", sep = ""), tre, extended = FALSE): unused
  argument(s) (extended = FALSE)
  phylog.permut : adddistances: possible error in
  sub(paste(nodes.names[i], ",", sep = ""), paste(nodes.names[i], ":",
  phylog$nodes[i], ",", sep = ""), tre, extended = FALSE): unused
  argument(s) (extended = FALSE)
  phylog.permut : adddistances: possible error in
  sub(paste(nodes.names[i], ")", sep = ""), paste(nodes.names[i], ":",
  phylog$nodes[i], ")", sep = ""), tre, extended = FALSE): unused
  argument(s) (extended = FALSE)
  phylog.permut : permute: possible error in regexpr(paste(u1, "[,);]",
  sep = ""), tre, ext = FALSE): unused argument(s) (ext = FALSE)
  phylog.permut : permute: possible error in regexpr(paste(u2, "[,);]",
  sep = ""), tre, ext = FALSE): unused argument(s) (ext = FALSE)
  phylog.permut : permute: possible error in sub(paste(u1, lastcar1, sep
  = ""), "Restunlogicielformidable", tre, extended = FALSE): unused
  argument(s) (extended = FALSE)
  phylog.permut : permute: possible error in sub(paste(u2, lastcar2, sep
  = ""), paste(u1, lastcar2, sep = ""), tre, extended = FALSE): unused
  argument(s) (extended = FALSE)
  phylog.permut : permute: possible error in
  sub("Restunlogicielformidable", paste(u2, lastcar1, sep = ""), tre,
  extended = FALSE): unused argument(s) (extended = FALSE)
  plot.phylog: possible error in gsub("[_]", " ", labels.leaves, ext =
  FALSE): unused argument(s) (ext = FALSE)
  plot.phylog: possible error in gsub("[_]", " ", labels.nodes, ext =
  FALSE): unused argument(s) (ext = FALSE)
  radial.phylog: possible error in gsub("[_]", " ", labels.leaves, ext =
  FALSE): unused argument(s) (ext = FALSE)
  radial.phylog: possible error in gsub("[_]", " ", labels.nodes, ext =
  FALSE): unused argument(s) (ext = FALSE)
  taxo2phylog: possible error in sub(",)", ")", res, ext = FALSE): unused
  argument(s) (ext = FALSE)
  taxo2phylog: possible error in sub(",)", ")", w, ext = FALSE): unused
  argument(s) (ext = FALSE)
  taxo2phylog: possible error in gsub(old, w, res, ext = FALSE): unused
  argument(s) (ext = FALSE)
• checking Rd files ... WARNING
  checkRd: (5) s.value.Rd:29: Tag \code is invalid in a \code block
• checking Rd metadata ... OK
• checking Rd cross-references ... WARNING
  Missing link(s) in documentation object './man/multispati.Rd':
  ‘[spdep]{listw}’
  
  Missing link(s) in documentation object './man/multispati.randtest.Rd':
  ‘[spdep]{listw}’
  
  Missing link(s) in documentation object './man/multispati.rtest.Rd':
  ‘[spdep]{listw}’
  
  Missing link(s) in documentation object './man/variance.phylog.Rd':
  ‘[base]{lm}’
  
  See the information in section 'Cross-references' of the 'Writing R
  Extensions' manual.
  
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking data for non-ASCII characters ... 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 ... OK
• checking examples ... ERROR
  Running examples in 'ade4-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * EH
  >
  > flush(stderr()); flush(stdout())
  >
  > ### Name: EH
  > ### Title: Amount of Evolutionary History
  > ### Aliases: EH
  > ### Keywords: multivariate
  >
  > ### ** Examples
  >
  > data(carni70)
  > carni70.phy <- newick2phylog(carni70$tre)
  Error in gsub(" ", "", x.tre, ext = FALSE) :
  unused argument(s) (ext = FALSE)
  Calls: newick2phylog -> complete -> gsub
  Execution halted