* using log directory 'd:/Rcompile/CRANpkg/local/2.15/compositions.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 '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 whether package 'compositions' 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
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'
acompGOF.test.formula: no visible global function definition for
  'codes'
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'
Found .Internal calls in the following functions:
  'cor.default' 'cov.default' 'tryDebugger' 'var.default'
with calls to .Internal functions
  'cor' 'cov' '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 ...
** 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 'AitchisonTest.R'
  Running 'CheckGeometry.R'
  Running 'RobustTest.R'
  Running 'TestMissing.R'
  Running 'TestSimp.R'
  Running 'acheck.R'
  Running 'geostat.R'
  Running 'missings.R'
  Running 'quickcheck.R'
  Running 'tests.R'
** running tests for arch 'x64' OK
  Running 'AitchisonTest.R'
  Running 'CheckGeometry.R'
  Running 'RobustTest.R'
  Running 'TestMissing.R'
  Running 'TestSimp.R'
  Running 'acheck.R'
  Running 'geostat.R'
  Running 'missings.R'
  Running 'quickcheck.R'
  Running 'tests.R'
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/compositions.Rcheck/00check.log'
for details.