• using R Under development (unstable) (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• 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 for executable files ... 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 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 ... OK
• checking R code for possible problems ... WARNING
  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 ... NOTE
  Package(s) unavailable to check Rd xrefs: ‘GeneticsDesign’
• 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 ... [18s/18s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [3s/3s] OK
  Running ‘ci.balance.R’ [1s/1s]
  Running ‘makeGenotype_with_sep.R’ [1s/1s]
  Running ‘test.NA.R’ [1s/1s]
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 4 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/genetics.Rcheck/00check.log’
  for details.