* using log directory 'd:/Rcompile/CRANpkg/local/3.3/HBSTM.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'HBSTM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HBSTM' version '1.0.1'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'HBSTM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over 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 use of S3 registration ... OK
* checking 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
[,Autoregressive-character-missing-missing: warning in switch(EXP = i,
  avect = return(x@avect), a0vect = return(x@a0vect), a0L =
  return(x@a0L), spatialA = return(x@spatialA), sigma2A =
  return(x@sigma2A), H = return(x@H), subdiag = return(x@subdiag),
  stop("Error: ", i, " is not a Autoregressive slot")): partial
  argument match of 'EXP' to 'EXPR'
[,Autoregressive0-character-missing-missing: warning in switch(EXP = i,
  a0L0 = return(x@a0L0), siga0L0 = return(x@siga0L0), sigma2A0 =
  return(x@sigma2A0), spatialA0 = return(x@spatialA0), subdiag0 =
  return(x@subdiag0), stop("Error: ", i, " is not a Autoregressive0
  slot")): partial argument match of 'EXP' to 'EXPR'
[,CosSinMatrix-character-missing-missing: warning in switch(EXP = i,
  cosMat = return(x@cosMat), sinMat = return(x@sinMat), littlecosMat =
  return(x@littlecosMat), littlesinMat = return(x@littlesinMat),
  stop("Error: ", i, " is not a CosSinMatrix slot")): partial argument
  match of 'EXP' to 'EXPR'
[,HBSTM-character-missing-missing: warning in switch(EXP = i,
  Parameters = return(x@Parameters), Hyperpriors =
  return(x@Hyperpriors), seed = return(x@seed), mse = return(x@mse),
  iterations = return(x@iterations), newGrid = return(x@newGrid), K =
  return(x@K), Zt = return(x@Zt), fitted = return(x@fitted), residuals
  = return(x@residuals), MCMCsamp = return(x@MCMCsamp), MCMCclass =
  return(x@MCMCclass), stop("Error: ", i, " is not a STmodel slot")):
  partial argument match of 'EXP' to 'EXPR'
[,Hyperpriors-character-missing-missing: warning in switch(EXP = i, Mu0
  = return(x@Mu0), Mt0 = return(x@Mt0), Xt0 = return(x@Xt0), sigma2Y0 =
  return(x@sigma2Y0), sigma2E0 = return(x@sigma2E0), stop("Error: ", i,
  " is not a Hyperpriors slot")): partial argument match of 'EXP' to
  'EXPR'
[,Mt-character-missing-missing: warning in switch(EXP = i, Mt =
  return(x@Mt), seas = return(x@seas), stop("Error: ", i, " is not a Mt
  slot")): partial argument match of 'EXP' to 'EXPR'
[,Mt0-character-missing-missing: warning in switch(EXP = i, seas0 =
  return(x@seas0), stop("Error: ", i, " is not a Mt0 slot")): partial
  argument match of 'EXP' to 'EXPR'
[,MtAux-character-missing-missing: warning in switch(EXP = i, seas =
  return(x@seas), stop("Error: ", i, " is not a MtAux slot")): partial
  argument match of 'EXP' to 'EXPR'
[,Mu-character-missing-missing: warning in switch(EXP = i, muvect =
  return(x@muvect), mu0vect = return(x@mu0vect), mu0L = return(x@mu0L),
  sigma2Mu = return(x@sigma2Mu), spatialMu = return(x@spatialMu),
  stop("Error: ", i, " is not a Mu slot")): partial argument match of
  'EXP' to 'EXPR'
[,Mu0-character-missing-missing: warning in switch(EXP = i, mu0L0 =
  return(x@mu0L0), sigmu0L0 = return(x@sigmu0L0), sigma2Mu0 =
  return(x@sigma2Mu0), spatialMu0 = return(x@spatialMu0), stop("Error:
  ", i, " is not a Mu0 slot")): partial argument match of 'EXP' to
  'EXPR'
[,Parameters-character-missing-missing: warning in switch(EXP = i, Mu =
  return(x@Mu), Mt = return(x@Mt), Xt = return(x@Xt), Yt =
  return(x@Yt), sigma2Y = return(x@sigma2Y), sigma2E =
  return(x@sigma2E), stop("Error: ", i, " is not a Parameters slot")):
  partial argument match of 'EXP' to 'EXPR'
[,Seas-character-missing-missing: warning in switch(EXP = i, w =
  return(x@w), fvect = return(x@fvect), f0L = return(x@f0L), gvect =
  return(x@gvect), g0L = return(x@g0L), stop("Error: ", i, " is not a
  Seas slot")): partial argument match of 'EXP' to 'EXPR'
[,Seas0-character-missing-missing: warning in switch(EXP = i, sigf0L0 =
  return(x@sigf0L0), f0L0 = return(x@f0L0), sigg0L0 =
  return(x@sigg0L0), g0L0 = return(x@g0L0), stop("Error: ", i, " is not
  a Seas0 slot")): partial argument match of 'EXP' to 'EXPR'
[,SpatC-character-missing-missing: warning in switch(EXP = i, Matalpha
  = return(x@Matalpha), Matbeta = return(x@Matbeta), Matphi =
  return(x@Matphi), Mattheta = return(x@Mattheta), stop("Error: ", i, "
  is not a SpatC slot")): partial argument match of 'EXP' to 'EXPR'
[,SpatH-character-missing-missing: warning in switch(EXP = i, west =
  return(x@west), east = return(x@east), north = return(x@north), south
  = return(x@south), southwest = return(x@southwest), northeast =
  return(x@northeast), southeast = return(x@southeast), northwest =
  return(x@northwest), stop("Error: ", i, " is not a SpatH slot")):
  partial argument match of 'EXP' to 'EXPR'
[,SpatParam-character-missing-missing: warning in switch(EXP = i, alpha
  = return(x@alpha), beta = return(x@beta), phi = return(x@phi), theta
  = return(x@theta), Cmat = return(x@Cmat), lags = return(x@lags), dirs
  = return(x@dirs), stop("Error: ", i, " is not a SpatParam slot")):
  partial argument match of 'EXP' to 'EXPR'
[,SpatParam0-character-missing-missing: warning in switch(EXP = i,
  alpha0 = return(x@alpha0), beta0 = return(x@beta0), phi0 =
  return(x@phi0), theta0 = return(x@theta0), stop("Error: ", i, " is
  not a SpatParam0 slot")): partial argument match of 'EXP' to 'EXPR'
[,VectSubdiag-character-missing-missing: warning in switch(EXP = i,
  east = return(x@east), west = return(x@west), north =
  return(x@north), south = return(x@south), southeast =
  return(x@southeast), northwest = return(x@northwest), southwest =
  return(x@southwest), northeast = return(x@northeast), lags =
  return(x@lags), dirs = return(x@dirs), stop("Error: ", i, " is not a
  VectSubdiag slot")): partial argument match of 'EXP' to 'EXPR'
[,VectSubdiag0-character-missing-missing: warning in switch(EXP = i,
  east0 = return(x@east0), west0 = return(x@west0), north0 =
  return(x@north0), south0 = return(x@south0), southeast0 =
  return(x@southeast0), northwest0 = return(x@northwest0), southwest0 =
  return(x@southwest0), northeast0 = return(x@northeast0), stop("Error:
  ", i, " is not a VectSubdiag0 slot")): partial argument match of
  'EXP' to 'EXPR'
[,Xt-character-missing-missing: warning in switch(EXP = i, Xt =
  return(x@Xt), X0 = return(x@X0), sigma2N = return(x@sigma2N), AR =
  return(x@AR), templags = return(x@templags), stop("Error: ", i, " is
  not a Xt slot")): partial argument match of 'EXP' to 'EXPR'
[,Xt0-character-missing-missing: warning in switch(EXP = i, X00 =
  return(x@X00), sigma2X00 = return(x@sigma2X00), AR0 = return(x@AR0),
  sigma2N0 = return(x@sigma2N0), stop("Error: ", i, " is not a Xt0
  slot")): partial argument match of 'EXP' to 'EXPR'
[<-,Autoregressive-character-missing: warning in switch(EXP = i, avect
  = x@avect <- value, a0vect = x@a0vect <- value, a0L = x@a0L <- value,
  spatialA = x@spatialA <- value, sigma2A = x@sigma2A <- value, H = x@H
  <- value, subdiag = x@subdiag <- value): partial argument match of
  'EXP' to 'EXPR'
[<-,Autoregressive0-character-missing: warning in switch(EXP = i, a0L0
  = x@a0L0 <- value, siga0L0 = x@siga0L0 <- value, sigma2A0 =
  x@sigma2A0 <- value, spatialA0 = x@spatialA0 <- value, subdiag0 =
  x@subdiag0 <- value): partial argument match of 'EXP' to 'EXPR'
[<-,CosSinMatrix-character-missing: warning in switch(EXP = i, cosMat =
  x@cosMat <- value, sinMat = x@sinMat <- value, littlecosMat =
  x@littlecosMat <- value, littlesinMat = x@littlesinMat <- value):
  partial argument match of 'EXP' to 'EXPR'
[<-,HBSTM-character-missing: warning in switch(EXP = i, Parameters =
  x@Parameters <- value, Hyperpriors = x@Hyperpriors <- value, seed =
  x@seed <- value, mse = x@mse <- value, iterations = x@iterations <-
  value, newGrid = x@newGrid <- value, K = x@K <- value, Zt = x@Zt <-
  value, fitted = x@fitted <- value, residuals = x@residuals <- value,
  MCMCsamp = x@MCMCsamp <- value, MCMCclass = x@MCMCclass <- value):
  partial argument match of 'EXP' to 'EXPR'
[<-,Hyperpriors-character-missing: warning in switch(EXP = i, Mu0 =
  x@Mu0 <- value, Mt0 = x@Mt0 <- value, Xt0 = x@Xt0 <- value, sigma2Y0
  = x@sigma2Y0 <- value, sigma2E0 = x@sigma2E0 <- value): partial
  argument match of 'EXP' to 'EXPR'
[<-,Mt-character-missing: warning in switch(EXP = i, Mt = x@Mt <-
  value, seas = x@seas <- value): partial argument match of 'EXP' to
  'EXPR'
[<-,Mt0-character-missing: warning in switch(EXP = i, seas0 = x@seas0
  <- value): partial argument match of 'EXP' to 'EXPR'
[<-,MtAux-character-missing: warning in switch(EXP = i, seas = x@seas
  <- value): partial argument match of 'EXP' to 'EXPR'
[<-,Mu-character-missing: warning in switch(EXP = i, muvect = x@muvect
  <- value, mu0vect = x@mu0vect <- value, mu0L = x@mu0L <- value,
  sigma2Mu = x@sigma2Mu <- value, spatialMu = x@spatialMu <- value):
  partial argument match of 'EXP' to 'EXPR'
[<-,Mu0-character-missing: warning in switch(EXP = i, mu0L0 = x@mu0L0
  <- value, sigmu0L0 = x@sigmu0L0 <- value, sigma2Mu0 = x@sigma2Mu0 <-
  value, spatialMu0 = x@spatialMu0 <- value): partial argument match of
  'EXP' to 'EXPR'
[<-,Parameters-character-missing: warning in switch(EXP = i, Mu = x@Mu
  <- value, Mt = x@Mt <- value, Xt = x@Xt <- value, Yt = x@Yt <- value,
  sigma2Y = x@sigma2Y <- value, sigma2E = x@sigma2E <- value): partial
  argument match of 'EXP' to 'EXPR'
[<-,Seas-character-missing: warning in switch(EXP = i, w = x@w <-
  value, fvect = x@fvect <- value, f0L = x@f0L <- value, gvect =
  x@gvect <- value, g0L = x@g0L <- value): partial argument match of
  'EXP' to 'EXPR'
[<-,Seas0-character-missing: warning in switch(EXP = i, sigf0L0 =
  x@sigf0L0 <- value, f0L0 = x@f0L0 <- value, sigg0L0 = x@sigg0L0 <-
  value, g0L0 = x@g0L0 <- value): partial argument match of 'EXP' to
  'EXPR'
[<-,SpatC-character-missing: warning in switch(EXP = i, Matalpha =
  x@Matalpha <- value, Matbeta = x@Matbeta <- value, Matphi = x@Matphi
  <- value, Mattheta = x@Mattheta <- value): partial argument match of
  'EXP' to 'EXPR'
[<-,SpatH-character-missing: warning in switch(EXP = i, west = x@west
  <- value, east = x@east <- value, north = x@north <- value, south =
  x@south <- value, southwest = x@southwest <- value, northeast =
  x@northeast <- value, southeast = x@southeast <- value, northwest =
  x@northwest <- value): partial argument match of 'EXP' to 'EXPR'
[<-,SpatParam-character-missing: warning in switch(EXP = i, alpha =
  x@alpha <- value, beta = x@beta <- value, phi = x@phi <- value, theta
  = x@theta <- value, Cmat = x@Cmat <- value, lags = x@lags <- value,
  dirs = x@dirs <- value): partial argument match of 'EXP' to 'EXPR'
[<-,SpatParam0-character-missing: warning in switch(EXP = i, alpha0 =
  x@alpha0 <- value, beta0 = x@beta0 <- value, phi0 = x@phi0 <- value,
  theta0 = x@MatTheta <- value): partial argument match of 'EXP' to
  'EXPR'
[<-,VectSubdiag-character-missing: warning in switch(EXP = i, east =
  x@east <- value, west = x@west <- value, north = x@north <- value,
  south = x@south <- value, southeast = x@southeast <- value, northwest
  = x@northwest <- value, southwest = x@southwest <- value, northeast =
  x@northeast <- value, lags = x@lags <- value, dirs = x@dirs <-
  value): partial argument match of 'EXP' to 'EXPR'
[<-,VectSubdiag0-character-missing: warning in switch(EXP = i, east0 =
  x@east0 <- value, west0 = x@west0 <- value, north0 = x@north0 <-
  value, south0 = x@south0 <- value, southeast0 = x@southeast0 <-
  value, northwest0 = x@northwest0 <- value, southwest0 = x@southwest0
  <- value, northeast0 = x@northeast0 <- value): partial argument match
  of 'EXP' to 'EXPR'
[<-,Xt-character-missing: warning in switch(EXP = i, Xt = x@Xt <-
  value, X0 = x@X0 <- value, sigma2N = x@sigma2N <- value, AR = x@AR <-
  value, templags = x@templags <- value): partial argument match of
  'EXP' to 'EXPR'
[<-,Xt0-character-missing: warning in switch(EXP = i, X00 = x@X00 <-
  value, sigma2X00 = x@sigma2X00 <- value, AR0 = x@AR0 <- value,
  sigma2N0 = x@sigma2N0 <- value): partial argument match of 'EXP' to
  'EXPR'
.HBSTM.estim: no visible binding for global variable 'median'
.HBSTM.estim: no visible global function definition for 'median'
.HBSTM.fit: no visible global function definition for 'rnorm'
.HBSTM.fit: no visible global function definition for 'rgamma'
.HBSTM.fit: no visible global function definition for 'par'
.HBSTM.fit: no visible global function definition for 'plot'
.HBSTM.fit: no visible global function definition for 'ts'
.HBSTM.fit: no visible global function definition for 'lines'
.HBSTM.fit: no visible global function definition for 'legend'
.HBSTM.fit: no visible global function definition for 'acf'
.HBSTM.fit: no visible global function definition for 'pacf'
.HBSTM.fit: no visible binding for global variable 'sd'
.HBSTM.fit: no visible binding for global variable 'median'
.HBSTM.fit : <anonymous>: no visible global function definition for
  'quantile'
.HBSTM.plotFit: no visible global function definition for 'dev.new'
.HBSTM.plotFit: no visible global function definition for 'layout'
.HBSTM.resid.plot: no visible global function definition for 'dev.new'
.HBSTM.resid.plot: no visible global function definition for
  'layout.show'
.HBSTM.resid.plot: no visible global function definition for 'layout'
.HBSTM.resid.plot: no visible global function definition for 'hist'
.HBSTM.resid.plot: no visible global function definition for 'plot'
.HBSTM.resid.plot: no visible global function definition for 'abline'
.HBSTM.resid.plot: no visible global function definition for 'qqnorm'
.HBSTM.resid.plot: no visible global function definition for 'qqline'
.HBSTM.resid.plot: no visible global function definition for 'par'
.HBSTM.resid.plot: no visible global function definition for 'acf'
.HBSTM.resid.plot: no visible global function definition for 'pacf'
.results.HBSTM: no visible global function definition for 'jpeg'
.results.HBSTM: no visible global function definition for 'dev.new'
.results.HBSTM: no visible global function definition for 'par'
.results.HBSTM: no visible global function definition for 'mtext'
.results.HBSTM: no visible global function definition for 'layout.show'
.results.HBSTM: no visible global function definition for 'layout'
MHSpat: no visible global function definition for 'runif'
analysis.spatial: no visible global function definition for 'median'
analysis.spatial: no visible global function definition for 'quantile'
auxplotFit: no visible global function definition for 'image'
auxplotFit: no visible global function definition for 'topo.colors'
auxplotFit: no visible global function definition for 'contour'
estYt.check: no visible global function definition for 'object.size'
estYt.check: no visible global function definition for 'memory.limit'
graph: no visible global function definition for 'dev.off'
initialStand.creation: no visible global function definition for 'lm'
initialStand.creation: no visible global function definition for 'coef'
initialStand.creation: no visible global function definition for 'sd'
mat.aux: no visible global function definition for 'median'
mat.aux: no visible global function definition for 'quantile'
plotCI.aux: no visible global function definition for 'plot'
plotCI.aux: no visible global function definition for 'axis'
plotCI.aux: no visible global function definition for 'arrows'
plotCI.aux: no visible global function definition for 'points'
plotCI.spatial: no visible global function definition for 'jpeg'
plotCI.spatial: no visible global function definition for 'dev.new'
plotCI.spatial: no visible global function definition for 'par'
plotCI.spatial: no visible global function definition for 'layout'
plotCI.spatial: no visible global function definition for 'mtext'
save.check: no visible global function definition for 'object.size'
save.check: no visible global function definition for 'memory.limit'
truncNorm: no visible global function definition for 'rnorm'
truncNorm: no visible global function definition for 'rexp'
truncNorm: no visible global function definition for 'runif'
estimation,HBSTM: no visible binding for global variable 'median'
estimation,HBSTM: no visible global function definition for 'median'
hbstm.fit,HBSTM: no visible global function definition for 'rnorm'
hbstm.fit,HBSTM: no visible global function definition for 'rgamma'
hbstm.fit,HBSTM: no visible global function definition for 'par'
hbstm.fit,HBSTM: no visible global function definition for 'plot'
hbstm.fit,HBSTM: no visible global function definition for 'ts'
hbstm.fit,HBSTM: no visible global function definition for 'lines'
hbstm.fit,HBSTM: no visible global function definition for 'legend'
hbstm.fit,HBSTM: no visible global function definition for 'acf'
hbstm.fit,HBSTM: no visible global function definition for 'pacf'
hbstm.fit,HBSTM: no visible binding for global variable 'sd'
hbstm.fit,HBSTM: no visible binding for global variable 'median'
hbstm.fit,HBSTM : <anonymous>: no visible global function definition
  for 'quantile'
plotFit,HBSTM: no visible global function definition for 'dev.new'
plotFit,HBSTM: no visible global function definition for 'layout'
plotRes,HBSTM: no visible global function definition for 'dev.new'
plotRes,HBSTM: no visible global function definition for 'layout.show'
plotRes,HBSTM: no visible global function definition for 'layout'
plotRes,HBSTM: no visible global function definition for 'hist'
plotRes,HBSTM: no visible global function definition for 'plot'
plotRes,HBSTM: no visible global function definition for 'abline'
plotRes,HBSTM: no visible global function definition for 'qqnorm'
plotRes,HBSTM: no visible global function definition for 'qqline'
plotRes,HBSTM: no visible global function definition for 'par'
plotRes,HBSTM: no visible global function definition for 'acf'
plotRes,HBSTM: no visible global function definition for 'pacf'
results,HBSTM: no visible global function definition for 'jpeg'
results,HBSTM: no visible global function definition for 'dev.new'
results,HBSTM: no visible global function definition for 'par'
results,HBSTM: no visible global function definition for 'mtext'
results,HBSTM: no visible global function definition for 'layout.show'
results,HBSTM: no visible global function definition for 'layout'
Undefined global functions or variables:
  abline acf arrows axis coef contour dev.new dev.off hist image jpeg
  layout layout.show legend lines lm median memory.limit mtext
  object.size pacf par plot points qqline qqnorm quantile rexp rgamma
  rnorm runif sd topo.colors ts
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "jpeg", "topo.colors")
  importFrom("graphics", "abline", "arrows", "axis", "contour", "hist",
             "image", "layout", "layout.show", "legend", "lines",
             "mtext", "par", "plot", "points")
  importFrom("stats", "acf", "coef", "lm", "median", "pacf", "qqline",
             "qqnorm", "quantile", "rexp", "rgamma", "rnorm", "runif",
             "sd", "ts")
  importFrom("utils", "memory.limit", "object.size")
to your NAMESPACE file.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [1s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs