* using log directory 'd:/Rcompile/CRANpkg/local/2.15/adegenet.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'adegenet/DESCRIPTION' ... OK
* this is package 'adegenet' version '1.3-4'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'multicore'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'adegenet' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data    1.3Mb
    doc     2.8Mb
    files   1.6Mb
* checking package directory ... OK
* checking for portable file names ... 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 'x64'
** 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 ... NOTE
Found the following possibly unsafe calls:
File 'R/haploGen.R':
  found unlockBinding("as.list.DNAbin", env)
  found assignInNamespace("as.list.DNAbin", as.list.DNAbin.new, ns =
    "ape", envir = env)
assignplot: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
assignplot: warning in axis(side = 1, at = 1:n.grp, tick = FALSE, label
  = colnames(x$posterior)): partial argument match of 'label' to
  'labels'
assignplot: warning in axis(side = 2, at = seq(0.5, by = 1, le =
  n.ind), label = rev(rownames(x$posterior)), las = 1, cex.axis =
  cex.lab): partial argument match of 'label' to 'labels'
chooseCN: warning in require(spdep, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
chooseCN: warning in require(tripack, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
chooseCN: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
compoplot: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
dapc.data.frame: warning in require(ade4, quiet = TRUE): partial
  argument match of 'quiet' to 'quietly'
dapc.data.frame: warning in require(MASS, quiet = TRUE): partial
  argument match of 'quiet' to 'quietly'
dapc.genind: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
dapc.genind: warning in require(MASS, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
dapc.genlight: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
dapc.genlight: warning in require(MASS, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
fasta2genlight: no visible global function definition for 'mclapply'
find.clusters.data.frame: warning in require(ade4, quiet = TRUE):
  partial argument match of 'quiet' to 'quietly'
find.clusters.data.frame: warning in require(MASS, quiet = TRUE):
  partial argument match of 'quiet' to 'quietly'
find.clusters.genind: warning in require(ade4, quiet = TRUE): partial
  argument match of 'quiet' to 'quietly'
find.clusters.genind: warning in require(MASS, quiet = TRUE): partial
  argument match of 'quiet' to 'quietly'
find.clusters.genlight: warning in require(ade4, quiet = TRUE): partial
  argument match of 'quiet' to 'quietly'
find.clusters.genlight: warning in require(MASS, quiet = TRUE): partial
  argument match of 'quiet' to 'quietly'
glPca: no visible global function definition for 'mclapply'
glPlot: warning in axis(side = 2, at = nInd(x) - ylabpos + 1, lab =
  ylabpos): partial argument match of 'lab' to 'labels'
loadingplot.default: warning in jitter(x.ann, fac = lab.jitter):
  partial argument match of 'fac' to 'factor'
loadingplot.default: warning in jitter(y.ann, fac = lab.jitter):
  partial argument match of 'fac' to 'factor'
monmonier: warning in sort(unique(D)[unique(D) > 0], dec = TRUE):
  partial argument match of 'dec' to 'decreasing'
optimize.monmonier: warning in sort(unique(D)[unique(D) > 0], dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
optimize.monmonier: warning in monmonier(xy, dist, cn.nb, skip = i,
  scanthres = FALSE, threshold = Dlim, bd.length = bd.length, allowLoop
  = allowLoop): partial argument match of 'skip' to 'skip.local.diff'
plot.monmonier: warning in s.value(xy, variable, grid = FALSE,
  include.ori = FALSE, addaxes = FALSE, neig = neig, cneig = cneig,
  clegend = clegend, csize = csize, cpoint = cpoint, pch = 20, pixmap =
  pixmap, method = method, sub = sub, csub = csub, possub = possub,
  add.plot = add.plot): partial argument match of 'include.ori' to
  'include.origin'
plot.spca: warning in s.label(xy, clab = clab, include.ori = FALSE,
  addaxes = FALSE, neig = neig, cneig = 1, sub = "Connection network",
  csub = 2): partial argument match of 'clab' to 'clabel'
plot.spca: warning in s.label(xy, clab = clab, include.ori = FALSE,
  addaxes = FALSE, neig = neig, cneig = 1, sub = "Connection network",
  csub = 2): partial argument match of 'include.ori' to
  'include.origin'
plot.spca: warning in s.image(xy, z, include.ori = FALSE, grid = TRUE,
  kgrid = 10, cgrid = 1, sub = sub, csub = csub, possub =
  "bottomleft"): partial argument match of 'include.ori' to
  'include.origin'
plot.spca: warning in s.value(xy, z, include.ori = FALSE, addaxes =
  FALSE, clegend = 0, csize = 0.6, neig = neig, sub = sub, csub = csub,
  possub = "bottomleft"): partial argument match of 'include.ori' to
  'include.origin'
plot.spca: warning in s.value(xy, z, include.ori = FALSE, addaxes =
  FALSE, clegend = 0, csize = 0.6, method = "greylevel", neig = neig,
  sub = sub, csub = csub, possub = "bottomleft"): partial argument
  match of 'include.ori' to 'include.origin'
read.PLINK: no visible global function definition for 'mclapply'
read.genepop: warning in sort(splited, dec = TRUE): partial argument
  match of 'dec' to 'decreasing'
read.snp: no visible global function definition for 'mclapply'
repool: warning in unlist(listPop, use.name = FALSE): partial argument
  match of 'use.name' to 'use.names'
scatter.dapc: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
scatter.dapc: warning in add.scatter(inset(), posi = posi.da, ratio =
  ratio.da, bg = bg.inset, inset = inset.da): partial argument match of
  'bg' to 'bg.col'
scatter.dapc: warning in add.scatter(inset(), posi = posi.pca, ratio =
  ratio.pca, bg = bg.inset, inset = inset.pca): partial argument match
  of 'bg' to 'bg.col'
scatter.glPca: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
spca: warning in require(ade4, quiet = TRUE): partial argument match of
  'quiet' to 'quietly'
spca: warning in require(spdep, quiet = TRUE): partial argument match
  of 'quiet' to 'quietly'
summary.dapc: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
* 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 'd:/Rcompile/CRANpkg/lib/2.15/adegenet/libs/i386/adegenet.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'snpbin.o'
File 'd:/Rcompile/CRANpkg/lib/2.15/adegenet/libs/x64/adegenet.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'snpbin.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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 ... OK
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/adegenet.Rcheck/00check.log'
for details.