* using log directory 'd:/Rcompile/CRANpkg/local/2.13/kernelPop.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'kernelPop/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'kernelPop' version '0.11.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'kernelPop' 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
landscape.tajima.d: no visible global function definition for 'theta.k'
landscape.tajima.d: no visible global function definition for 'theta.s'
landscape.theta.h: no visible global function definition for 'theta.h'
landscape.theta.k: no visible global function definition for 'theta.k'
landscape.theta.s: no visible global function definition for 'theta.s'
* 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 ... WARNING
Assignments in \usage in documentation object 'SimulationComponents':
  rland <- landscape.advance(rland = l)
  rland <- landscape.carry(rland = l)
  rland <- landscape.extinct(rland = l)
  rland <- landscape.reproduce(rland = l)
  rland <- landscape.survive(rland = l)

Assignments in \usage in documentation object 'landscape.FWright':
  Fmat <- landscape.FWright(rland)

Assignments in \usage in documentation object 'landscape.Fst':
  Fstmat <- landscape.Fst(rland, verb = F)

Assignments in \usage in documentation object 'landscape.allelecount':
  hetmat <- landscape.exp.het(rland, tbl.out = F)

Assignments in \usage in documentation object 'landscape.allelefreq':
  hetmat <- landscape.allelefreq(rland, tbl.out = F)

Assignments in \usage in documentation object 'landscape.clean':
  rland <- landscape.clean(rland)

Assignments in \usage in documentation object 'landscape.coalinput':
  rland <- landscape.coalinput(rland, npp = 500, arlseq = "seq.arp", 
      arlms = "ms.arp", seqsitemut = 1e-07, msmut = 5e-04)

Assignments in \usage in documentation object 'landscape.demography':
  rland <- landscape.demography(rland)

Assignments in \usage in documentation object 'landscape.exp.het':
  hetmat <- landscape.exp.het(rland)

Assignments in \usage in documentation object 'landscape.new.landscape':
  rland <- landscape.new.empty()

Assignments in \usage in documentation object 'landscape.new.epoch':
  rland <- landscape.new.epoch(rland, S = NULL, R = NULL, M = NULL, 
      epochprob = 1, startgen = 0, extinct = NULL, carry = NULL, 
      localprob = NULL, pollen.kernels = NULL, seed.kernels = NULL, 
      leftx = NULL, rightx = NULL, boty = NULL, topy = NULL, maxland = c(0, 
          0, 10000, 10000))

Assignments in \usage in documentation object 'landscape.new.example':
  rland <- landscape.new.example()

Assignments in \usage in documentation object 'landscape.new.floatparam':
  rland <- landscape.new.floatparam(rland, s = 0, seedscale = c(10, 
      10), seedshape = c(10, 10), seedmix = 1, pollenscale = c(2, 
      10), pollenshape = c(2, 6), pollenmix = 1, asp = 1)

Assignments in \usage in documentation object 'landscape.new.individuals':
  rland <- landscape.new.individuals(rland, PopulationSizes)

Assignments in \usage in documentation object 'landscape.new.intparam':
  rland <- landscape.new.intparam(rland, h = 2, s = 1, cg = 0, 
      ce = 0, totgen = 500, maxland = 10000)

Assignments in \usage in documentation object 'landscape.new.local.demo':
  rland <- landscape.new.local.demo(rland, S = Smatrix, R = Rmatrix, 
      M = Mmatrix, k = 0)

Assignments in \usage in documentation object 'landscape.new.locus':
  rland <- landscape.new.locus(rland, type = 0, ploidy = 1, mutationrate = 0, 
      transmission = 1, numalleles = 2, allelesize = 50, frequencies = 0)

Assignments in \usage in documentation object 'landscape.new.switchparam':
  rland <- landscape.new.switchparam(rland, re = 1, rd = 1, mp = 1, 
      dd = 0)

Assignments in \usage in documentation object 'landscape.obs.het':
  hetmat <- landscape.obs.het(rland)

Assignments in \usage in documentation object 'landscape.simulate':
  rland <- landscape.simulate(rland = l, numit = 100, seed = -1, 
      compress = FALSE, adj.lambda = 0)

Assignments in \usage in documentation object 'landscape.theta.h':
  theta.h.mat <- landscape.theta.h(rland)

Assignments in \usage in documentation object 'landscape.theta.k':
  theta.k.mat <- landscape.theta.k(rland)

Assignments in \usage in documentation object 'landscape.theta.s':
  theta.s.mat <- landscape.theta.s(rland)

Assignments in \usage in documentation object 'landscape.to.rtheta':
  genin <- landscape.to.rtheta(Rland, numi)

Assignments in \usage in documentation object 'landscape.write.foreign':
  rland <- landscape.write.foreign(rland, fn = "foreign", numi = 24, 
      fmt = "GDA")

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 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 sizes of PDF files under inst/doc ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
  'd:/Rcompile/CRANpkg/local/2.13/kernelPop.Rcheck/00check.log'
for details