• using R version 3.1.0 (2014-04-10)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘geoR/DESCRIPTION’ ... OK
• this is package ‘geoR’ version ‘1.7-4’
• 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 for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘geoR’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• 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 dependencies in R code ... NOTE
  ':::' call which should be '::': ‘scatterplot3d:::scatterplot3d’
  See the note in ?`:::` about the use of this operator.
  There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.check.cov.model’
  See the information on DESCRIPTION files in the chapter ‘Creating R
  packages’ of the ‘Writing R Extensions’ manual.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... NOTE
  Calls with DUP = FALSE:
  .C("cor_diag", as.double(coords[, 1]), as.double(coords[, 2]),
  as.integer(nc), as.integer(.cor.number(cov.model)), as.double(phi),
  as.double(kappa), out, DUP = FALSE, PACKAGE = "geoR")
  .C("distdiag", as.double(coords[, 1]), as.double(coords[, 2]),
  as.integer(nc), out, DUP = FALSE, PACKAGE = "geoR")
  .C("loccoords", as.double(as.vector(locations[, 1])), as.double(as.vector(locations[,
  2])), as.double(as.vector(coords[, 1])), as.double(as.vector(coords[,
  2])), as.integer(nl), as.integer(nc), out, DUP = FALSE, PACKAGE = "geoR")
  DUP = FALSE is deprecated and may be disabled in future versions of R.
• checking R code for possible problems ... NOTE
  Found the following assignments to the global environment:
  File ‘geoR/R/auxiliar.R’:
  assign(".objfuncQQ", objfunc, pos = 1)
  assign(".bounds.list", .bounds.list, pos = 1)
  assign("madtonormalQQ", madtonormalQQ, pos = 1)
  File ‘geoR/R/likGRF.R’:
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords),
  realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords),
  realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords.c),
  temp.list$realisations), vecdist), pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
  File ‘geoR/R/likOLD.R’:
  assign(".temp.list", list(z = z, xmat = xmat, txmat = txmat,
  fixtau = fixtau, ftau = ftau, method = method, kappa = kappa,
  cov.model = cov.model, beta.size = beta.size, lower.phi = lower.phi,
  dists.lowertri = dists.vec, var.z = var.z, fix.lambda = fix.lambda,
  n = n, minimisation.function = minimisation.function), pos = 1)
  assign(".temp.lower", c(0, lower.phi), pos = 1)
  assign(".temp.lower", c(0, lower.phi), pos = 1)
  assign(".ind.prof.phi", 2, pos = 1)
  assign(".temp.lower", c(0, lower.phi), pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
  assign(".ind.prof.phi", 2, pos = 1)
  assign(".temp.lower", c(0, lower.phi), pos = 1)
  assign(".ind.prof.phi", 2, pos = 1)
  assign(".temp.lower", c(0, lower.phi), pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
  assign(".ind.prof.phi", 2, pos = 1)
  assign(".temp.lower.phi", lower.phi, pos = 1)
  assign(".ind.prof.phi", 1, pos = 1)
  assign(".temp.lower.phi", lower.phi, pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
  assign(".temp.lower.phi", lower.phi, pos = 1)
  assign(".ind.prof.phi", 1, pos = 1)
  assign(".temp.lower.phi", lower.phi, pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
  assign(".ind.prof.phi", 1, pos = 1)
  assign(".temp.sill", theta[1], pos = 1)
  assign(".temp.phi", theta[2], pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.nugget", theta[1], pos = 1)
  assign(".temp.phi", theta[2], pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.phi", phi, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  File ‘geoR/R/profiles.R’:
  assign(".temp.list", list(n = n, z = data, beta.size = dim(trend)[2],
  kappa = obj.likfit$kappa, xmat = trend, method.lik = obj.likfit$method.lik,
  dists.lowertri = dists.vec, cov.model = obj.likfit$cov.model,
  fix.lambda = obj.likfit$transform.info$fix.lambda, lambda = obj.likfit$lambda,
  lower.phi = lower.phi, upper.phi = upper.phi, lower.sigmasq = lower.sigmasq,
  phi.est = phi, tausq.rel.est = tausq.rel, tausq.est = tausq,
  sigmasq.est = sigmasq), pos = 1)
  assign(".temp.temp.list", get(".temp.list", pos = 1), pos = 1)
  assign(".temp.list", .temp.temp.list, pos = 1)
  File ‘geoR/R/simul.R’:
  assign("setRF", geoR2RF(cov.model = cov.model, cov.pars = cov.pars,
  nugget = nugget, kappa = kappa, aniso.pars = aniso.pars),
  pos = 1)
  File ‘geoR/R/variofit.R’:
  assign(".temp.theta", NULL, pos = 1)
  assign(".temp.theta", theta, pos = 1)
  assign(".IND.geoR.variog.model.env", TRUE, pos = 1)
  File ‘geoR/R/variogram.R’:
  assign(".variog4.nomessage", TRUE, pos = 1)
• 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [13s/13s] OK
• checking PDF version of manual ... OK

NOTE: There were 3 notes.