* using log directory 'd:/Rcompile/CRANpkg/local/2.15/spectralGP.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 'spectralGP/DESCRIPTION' ... OK
* this is package 'spectralGP' version '1.3'
* 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 'spectralGP' 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
File 'spectralGP/R/onLoad.R':
  .onLoad calls:
    cat("Package spectralGP (1.3) is loaded.\n===============================================================\n WARNING: spectralGP uses objects in the form of environments,\n thereby passing by reference.  Various method functions make\n changes to the input gp object as a side effect, thereby\n changing the object in the calling environment, and\n returning NULL.\n===============================================================",     fill = FALSE)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in ?.onAttach.

Gibbs.sample.coeff.gp: warning in matrix(2 * sdVal * sdVal/sig2e, nr =
  m1, nc = m2): partial argument match of 'nr' to 'nrow'
Gibbs.sample.coeff.gp: warning in matrix(2 * sdVal * sdVal/sig2e, nr =
  m1, nc = m2): partial argument match of 'nc' to 'ncol'
Gibbs.sample.coeff.gp: warning in fft(matrix((z - meanVal)/sdVal, nr =
  m1, nc = m2, byrow = FALSE), inv = FALSE): partial argument match of
  'inv' to 'inverse'
Gibbs.sample.coeff.gp: warning in matrix((z - meanVal)/sdVal, nr = m1,
  nc = m2, byrow = FALSE): partial argument match of 'nr' to 'nrow'
Gibbs.sample.coeff.gp: warning in matrix((z - meanVal)/sdVal, nr = m1,
  nc = m2, byrow = FALSE): partial argument match of 'nc' to 'ncol'
Gibbs.sample.coeff.gp: warning in matrix(rnorm(m1 * m2, Re(coeff.mean),
  sqrt(c(coeff.var))), nr = m1, nc = m2): partial argument match of
  'nr' to 'nrow'
Gibbs.sample.coeff.gp: warning in matrix(rnorm(m1 * m2, Re(coeff.mean),
  sqrt(c(coeff.var))), nr = m1, nc = m2): partial argument match of
  'nc' to 'ncol'
Gibbs.sample.coeff.gp: warning in matrix(rnorm(m1 * m2, Im(coeff.mean),
  sqrt(c(coeff.var))), nr = m1, nc = m2): partial argument match of
  'nr' to 'nrow'
Gibbs.sample.coeff.gp: warning in matrix(rnorm(m1 * m2, Im(coeff.mean),
  sqrt(c(coeff.var))), nr = m1, nc = m2): partial argument match of
  'nc' to 'ncol'
Gibbs.sample.coeff.gp: warning in matrix(1, nr = m1, nc = m2): partial
  argument match of 'nr' to 'nrow'
Gibbs.sample.coeff.gp: warning in matrix(1, nr = m1, nc = m2): partial
  argument match of 'nc' to 'ncol'
Hastings.coeff.gp: warning in matrix(2 * sdVal * sdVal/sig2e, nr = m1,
  nc = m2): partial argument match of 'nr' to 'nrow'
Hastings.coeff.gp: warning in matrix(2 * sdVal * sdVal/sig2e, nr = m1,
  nc = m2): partial argument match of 'nc' to 'ncol'
Hastings.coeff.gp: warning in fft(matrix((z - meanVal)/sdVal, nr = m1,
  nc = m2, byrow = FALSE), inv = FALSE): partial argument match of
  'inv' to 'inverse'
Hastings.coeff.gp: warning in matrix((z - meanVal)/sdVal, nr = m1, nc =
  m2, byrow = FALSE): partial argument match of 'nr' to 'nrow'
Hastings.coeff.gp: warning in matrix((z - meanVal)/sdVal, nr = m1, nc =
  m2, byrow = FALSE): partial argument match of 'nc' to 'ncol'
Hastings.coeff.gp: warning in matrix(1, nr = m1, nc = m2): partial
  argument match of 'nr' to 'nrow'
Hastings.coeff.gp: warning in matrix(1, nr = m1, nc = m2): partial
  argument match of 'nc' to 'ncol'
add.blocks.gp: warning in matrix(1:object$gridsize[1], nc = 1): partial
  argument match of 'nc' to 'ncol'
add.blocks.gp: warning in matrix(object$blocks[[1]], nc = 2): partial
  argument match of 'nc' to 'ncol'
add.blocks.gp: warning in matrix(object$blocks[[b]], nc = 2): partial
  argument match of 'nc' to 'ncol'
calc.variances.gp: warning in matrix(object$specdens(object$omega,
  object$specdens.param, d = object$d), nr = object$gridsize[1], nc =
  object$gridsize[2], byrow = FALSE): partial argument match of 'nr' to
  'nrow'
calc.variances.gp: warning in matrix(object$specdens(object$omega,
  object$specdens.param, d = object$d), nr = object$gridsize[1], nc =
  object$gridsize[2], byrow = FALSE): partial argument match of 'nc' to
  'ncol'
copy.gp: warning in assign(elements[index], get(elements[index], env =
  object, inherits = FALSE), env = object2): partial argument match of
  'env' to 'envir'
copy.gp: warning in get(elements[index], env = object, inherits =
  FALSE): partial argument match of 'env' to 'envir'
gp: warning in matrix(0, nr = gridsize[1], nc = gridsize[2]): partial
  argument match of 'nr' to 'nrow'
gp: warning in matrix(0, nr = gridsize[1], nc = gridsize[2]): partial
  argument match of 'nc' to 'ncol'
gp: warning in matrix(omega1, nc = 1): partial argument match of 'nc'
  to 'ncol'
matern.specdens: warning in matrix(c(omega), nc = 1): partial argument
  match of 'nc' to 'ncol'
matern.specdens: warning in matrix(omega, nr = 1, nc = d): partial
  argument match of 'nr' to 'nrow'
matern.specdens: warning in matrix(omega, nr = 1, nc = d): partial
  argument match of 'nc' to 'ncol'
names.gp: warning in ls(env = x): partial argument match of 'env' to
  'envir'
updateprocess.gp: warning in fft(object$coeff, inv = TRUE): partial
  argument match of 'inv' to 'inverse'
xy2unit: warning in matrix(locations.scale, nc = 1): partial argument
  match of 'nc' to 'ncol'
xy2unit: warning in matrix(locations, nc = 1): partial argument match
  of 'nc' to 'ncol'
zero.coeff.gp: warning in matrix(0, nr = object$gridsize[1], nc =
  object$gridsize[2]): partial argument match of 'nr' to 'nrow'
zero.coeff.gp: warning in matrix(0, nr = object$gridsize[1], nc =
  object$gridsize[2]): 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 ... NOTE
S3 methods shown with full name in documentation object 'image.plot':
  'image.plot'

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 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/spectralGP.Rcheck/00check.log'
for details.