* using log directory 'd:/Rcompile/CRANpkg/local/2.15/genetics.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 'genetics/DESCRIPTION' ... OK
* this is package 'genetics' version '1.3.6'
* 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 whether package 'genetics' can be installed ... OK
* checking installed package size ... OK
* 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
HWE.chisq.genotype: warning in pchisq(test$statistic, test$parameter,
  lower = FALSE): partial argument match of 'lower' to 'lower.tail'
hapmcmc: warning in matrix(nr = B, nc = length(hap.set)): partial
  argument match of 'nr' to 'nrow'
hapmcmc: warning in matrix(nr = B, nc = length(hap.set)): partial
  argument match of 'nc' to 'ncol'
mourant: warning in matrix(c(91, 32, 5, 147, 78, 17, 85, 75, 7), nr =
  3): partial argument match of 'nr' to 'nrow'
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nr' to 'nrow'
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nc' to 'ncol'
pw: warning in matrix(c(1, pi, pi, 1), nr = 2): partial argument match
  of 'nr' to 'nrow'
pw: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2, sd2^2), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(1, pi, pi, 1), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2,
  sd2^2), nr = 2): partial argument match of 'nr' to 'nrow'
Found .Internal call in the following function:
  'order.default'
with calls to .Internal functions
  'order'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* checking Rd files ... NOTE
prepare_Rd: undocumented.Rd:25-26: Dropping empty section \usage
* 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 ... NOTE
S3 methods shown with full name in documentation object 'diseq':
  'diseq.ci'

S3 methods shown with full name in documentation object 'genotype':
  'as.genotype.allele.count'

S3 methods shown with full name in documentation object 'print.LD':
  'summary.LD.data.frame'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Rnews.sty', 'genetics_article.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' OK
  Running 'ci.balance.R'
  Running 'makeGenotype_with_sep.R'
  Running 'test.NA.R'
** running tests for arch 'x64' OK
  Running 'ci.balance.R'
  Running 'makeGenotype_with_sep.R'
  Running 'test.NA.R'
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/genetics.Rcheck/00check.log'
for details.