* using log directory '/CRANPkg/check/prabclus.Rcheck'
* using R version 2.1.1, 2005-06-20 
* checking for file 'prabclus/DESCRIPTION' ... OK
* this is package 'prabclus' version '1.0-2'
* checking if this is a source package ... OK
* checking whether package 'prabclus' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'autoconst':
autoconst
  Code: function(x, prange = c(0, 1), twostep = TRUE, step1 = 0.1,
                 step2 = 0.01, plot = TRUE, nperp = 4, ejprob = NULL,
                 species.fixed = TRUE, pdfnb = FALSE)
  Docs: function(x, prange = c(0, 1), twostep = TRUE, step1 = 0.1,
                 step2 = 0.01, plot = TRUE, nperp = 4, ejprob = NA,
                 species.fixed = TRUE, pdfnb = FALSE)

Codoc mismatches from documentation object 'con.regmat':
con.regmat
  Code: function(regmat, neighbors, count = FALSE)
  Docs: function(regmat, neighbors, count = TRUE)

Codoc mismatches from documentation object 'pop.sim':
pop.sim
  Code: function(regmat, neighbors, h0c = 1, times = 200, dist =
                 "kulczynski", teststat = "isovertice", testc = NULL,
                 n.species = ncol(regmat), specperreg = NULL,
                 regperspec = NULL, species.fixed = FALSE, pdfnb =
                 FALSE)
  Docs: function(regmat, neighbors, h0c = 1, times = 200, dist =
                 "kulczynski", teststat = "isovertice", testc = NA,
                 n.species = ncol(regmat), specperreg = NA, regperspec
                 = NA, species.fixed = FALSE, pdfnb = pdfnb)

Codoc mismatches from documentation object 'prabinit':
prabinit
  Code: function(file = NULL, prabmatrix = NULL, rows.are.species =
                 TRUE, neighborhood = "none", distance = "kulczynski",
                 toprab = FALSE, toprabp = 0.05, outc = 5.2)
  Docs: function(file = NA, prabmatrix = NA, rows.are.species = TRUE,
                 neighborhood = "none", distance = "kulczynski",
                 toprab = FALSE, toprabp = 0.05, outc = 5.2)

* checking Rd \usage sections ... OK
* creating prabclus-Ex.R ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: package 'mva' has been merged into 'stats'
  Warning: package 'mva' has been merged into 'stats'
  Warning: package 'mva' has been merged into 'stats'
Support for loading defunct former base packages may be removed as soon as
of the next release of R.
* checking tests ... OK
* creating prabclus-manual.tex ... OK
* checking prabclus-manual.tex ... OK