• using R Under development (unstable) (2012-08-11 r60235)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘compositions/DESCRIPTION’ ... OK
• this is package ‘compositions’ version ‘1.10-2’
• 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 for hidden files and directories ... OK
• checking whether package ‘compositions’ 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
  AitchisonDistributionIntegrals: warning in matrix(erg$beta, nr = D):
  partial argument match of 'nr' to 'nrow'
  AitchisonDistributionIntegrals: warning in matrix(erg$clrVar, nr = D,
  nc = D): partial argument match of 'nr' to 'nrow'
  AitchisonDistributionIntegrals: warning in matrix(erg$clrVar, nr = D,
  nc = D): partial argument match of 'nc' to 'ncol'
  CoDaDendrogram: warning in axis(side = 1, at = 1:ncol(X), lab =
  colnames(X)[Vo$order], las = 2, lty = 0): partial argument match of
  'lab' to 'labels'
  compOKriging: warning in matrix(1, nr = n): partial argument match of
  'nr' to 'nrow'
  compOKriging: warning in matrix(1, nr = nnew): partial argument match
  of 'nr' to 'nrow'
  parametricPosdefClrMat: warning in matrix(0, nr = D, nc = D): partial
  argument match of 'nr' to 'nrow'
  parametricPosdefClrMat: warning in matrix(0, nr = D, nc = D): partial
  argument match of 'nc' to 'ncol'
  parametricPosdefMat: warning in matrix(0, nr = D, nc = D): partial
  argument match of 'nr' to 'nrow'
  parametricPosdefMat: warning in matrix(0, nr = D, nc = D): partial
  argument match of 'nc' to 'ncol'
  rAitchison: warning in matrix(erg$erg, nr = n): partial argument match
  of 'nr' to 'nrow'
  acompGOF.test.formula: no visible global function definition for
  ‘codes’
  Found .Internal call in the following function:
  ‘tryDebugger’
  with calls to .Internal functions
  ‘menu’
  
  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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following files look like leftovers/mistakes:
  ‘UsingCompositions.aux’, ‘UsingCompositions.dvi’,
  ‘UsingCompositions.log’
  Please remove them from your package.
  The following files should probably not be installed:
  ‘UsingCompositions.tex’
  The following directories should probably not be installed:
  ‘auto’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [32s/32s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [32s/32s] OK
  Running ‘AitchisonTest.R’ [1s/1s]
  Running ‘CheckGeometry.R’ [12s/12s]
  Running ‘RobustTest.R’ [1s/1s]
  Running ‘TestMissing.R’ [11s/11s]
  Running ‘TestSimp.R’ [3s/3s]
  Running ‘acheck.R’ [0s/0s]
  Running ‘geostat.R’ [0s/0s]
  Running ‘missings.R’ [0s/0s]
  Running ‘quickcheck.R’ [0s/0s]
  Running ‘tests.R’ [1s/1s]
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There was 1 note.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/compositions.Rcheck/00check.log’
  for details.