• using R Under development (unstable) (2012-02-24 r58481)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'bqtl/DESCRIPTION' ... OK
• this is package 'bqtl' version '1.0-26'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
• checking whether package 'bqtl' 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
• 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 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
  %equiv%: warning in matrix(apply(t.x == t.y, 2, sum) == nr, nc = dm[2],
  dimnames = list(dimnames(x)[[2]], dimnames(y)[[2]])): partial
  argument match of 'nc' to 'ncol'
  lapadj: warning in matrix(mode.mat[cbind(c(loc.indx[, col.seq]),
  rep(modes.used, rep(nrx, ncx)))], nc = ncx): partial argument match
  of 'nc' to 'ncol'
  lapadj: warning in matrix(z$hess, nc = np): partial argument match of
  'nc' to 'ncol'
  make.analysis.obj: warning in matrix(c(1, 0, -1, -1, 1, -1), nc = 2,
  dimnames = list(marker.levels[1:3], c("add", "dom"))): partial
  argument match of 'nc' to 'ncol'
  make.analysis.obj: warning in matrix(c(1, -1), nc = 1, dimnames =
  list(marker.levels[1:2], NULL)): partial argument match of 'nc' to
  'ncol'
  make.analysis.obj: warning in matrix(NA, nr = dm.data[1], nc =
  sum(which.chromo)): partial argument match of 'nr' to 'nrow'
  make.analysis.obj: warning in matrix(NA, nr = dm.data[1], nc =
  sum(which.chromo)): partial argument match of 'nc' to 'ncol'
  make.loc.right: warning in matrix(0, nr = nrm, nc = ncm): partial
  argument match of 'nr' to 'nrow'
  make.loc.right: warning in matrix(0, nr = nrm, nc = ncm): partial
  argument match of 'nc' to 'ncol'
  make.marker.numeric: warning in matrix(level.numeric[char.frame], nc =
  dm[2], dimnames = list(NULL, names(marker.frame))): partial argument
  match of 'nc' to 'ncol'
  make.regressor.matrix: warning in matrix(c(-1, 1), nr = 2): partial
  argument match of 'nr' to 'nrow'
  make.state.matrix: warning in matrix(1/2, nc = 2, nr = 2): partial
  argument match of 'nr' to 'nrow'
  make.state.matrix: warning in matrix(1/2, nc = 2, nr = 2): partial
  argument match of 'nc' to 'ncol'
  make.state.matrix: warning in matrix(c(1, -1, -1, 1)/2, nc = 2):
  partial argument match of 'nc' to 'ncol'
  make.state.matrix: warning in matrix(c(diag(lp), rep(NA, if (lp == 2) 8
  else 9)), nr = lp): partial argument match of 'nr' to 'nrow'
  make.varcov: warning in matrix(casewt/sum(casewt), nr = 1): partial
  argument match of 'nr' to 'nrow'
  predict.linear.bayes: warning in matrix(coefs, nc = 1): partial
  argument match of 'nc' to 'ncol'
  summary.adj: warning in matrix(adj, nr = n.loc): partial argument match
  of 'nr' to 'nrow'
  summary.adj: warning in matrix(adj * hk.ratio, nr = n.loc): partial
  argument match of 'nr' to 'nrow'
  uniq.config: warning in matrix(swap.obj$config, nr =
  dim(swap.obj$config)[1]): partial argument match of 'nr' to 'nrow'
  varcov: warning in match.call(expand = TRUE): partial argument match of
  'expand' to 'expand.dots'
• 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 compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking examples ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x64' ... OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  'd:/Rcompile/CRANpkg/local/2.15/bqtl.Rcheck/00check.log'
  for details.