• using R Under development (unstable) (2012-05-22 r59401)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘bark/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘bark’ version ‘0.1-0’
• 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 ‘bark’ 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 ... NOTE
  bark: warning in matrix(x.train, nc = 1): partial argument match of
  'nc' to 'ncol'
  bark: warning in matrix(x.test, nc = 1): partial argument match of 'nc'
  to 'ncol'
  bark: warning in matrix(NA, nr = dim(x.train)[1], nkeep): partial
  argument match of 'nr' to 'nrow'
  bark: warning in matrix(NA, nr = dim(x.test)[1], nkeep): partial
  argument match of 'nr' to 'nrow'
  bark: warning in matrix(NA, nc = fixed$n + 1, nr = nkeep): partial
  argument match of 'nr' to 'nrow'
  bark: warning in matrix(NA, nc = fixed$n + 1, nr = nkeep): partial
  argument match of 'nc' to 'ncol'
  bark: warning in matrix(NA, nc = fixed$p, nr = nkeep): partial argument
  match of 'nr' to 'nrow'
  bark: warning in matrix(NA, nc = fixed$p, nr = nkeep): partial argument
  match of 'nc' to 'ncol'
  bark: warning in matrix(NA, nc = 1, nr = nkeep): partial argument match
  of 'nr' to 'nrow'
  bark: warning in matrix(NA, nc = 1, nr = nkeep): partial argument match
  of 'nc' to 'ncol'
  getdesign: warning in matrix(z, nc = length(isi)): partial argument
  match of 'nc' to 'ncol'
  getfulldesign: warning in matrix(z, nc = length(isi)): partial argument
  match of 'nc' to 'ncol'
  llike: warning in matrix(fullXX[, theta$nvec > 0], nc = sum(theta$nvec
  > 0)): partial argument match of 'nc' to 'ncol'
  matDel: warning in matrix(0, nr = 0, nc = dimmat[2]): partial argument
  match of 'nr' to 'nrow'
  matDel: warning in matrix(0, nr = 0, nc = dimmat[2]): partial argument
  match of 'nc' to 'ncol'
  matDel: warning in matrix(mat[-del, ], nr = 1): partial argument match
  of 'nr' to 'nrow'
  matDel: warning in matrix(mat[-del, ], nc = dimmat[2]): partial
  argument match of 'nc' to 'ncol'
  matUpd: warning in matrix(mat, nr = 1): partial argument match of 'nr'
  to 'nrow'
  sim.Circle: warning in matrix(runif(n * dim, min = -1, max = 1), nr =
  n): partial argument match of 'nr' to 'nrow'
  sim.Friedman1: warning in matrix(runif(n * 10, min = 0, max = 1), nc =
  10): partial argument match of 'nc' to 'ncol'
  updacc: warning in matrix(c(cur[[lencur]], 1), nr = 1): partial
  argument match of 'nr' to 'nrow'
  updatebeta: warning in matrix(fullXX[, theta$nvec > 0], nc =
  sum(theta$nvec > 0)): partial argument match of 'nc' to 'ncol'
  updatez: warning in matrix(fullXX[, theta$nvec > 0], nc =
  sum(theta$nvec > 0)): partial argument match of 'nc' to 'ncol'
• 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 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 ... OK
• checking examples ... [366s/516s] OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/bark.Rcheck/00check.log’
  for details.