* using log directory '/CRANPkg/check/bim.Rcheck'
* using R version 2.1.1, 2005-06-20 
* checking for file 'bim/DESCRIPTION' ... OK
* this is package 'bim' version '1.01-1'
* checking if this is a source package ... OK
* checking whether package 'bim' 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 'bim.effects':
plot.bim.effects
  Code: function(x, cross = bim.cross(x), nqtl = 1, pattern = NULL,
                 exact = FALSE, chr, bw = 2, qtl = bim.effects(x,
                 cross, nqtl, pattern, exact, , bw), cex = bim.cex(x),
                 level = 0.8, project = substitute(x), main = mains,
                 mfcol = c(2 + domhere, 1), ...)
  Docs: function(x, cross, nqtl = 1, pattern = NULL, exact = FALSE,
                 chr, bw = 2, qtl = <<see below>>, cex, level = 0.8,
                 project = <<see below>>, main = <<see below>>, mfcol
                 = <<see below>>, ...)
bim.effects
  Code: function(x, cross = bim.cross(x), nqtl = 1, pattern = NULL,
                 exact = FALSE, chr, bw = 2, qtl = bim.qtl(x, cross,
                 nqtl, pattern, exact, , bw))
  Docs: function(x, cross, nqtl = 1, pattern = NULL, exact = FALSE,
                 chr, bw = 2, qtl = <<see below>>)

Codoc mismatches from documentation object 'bim.fdr':
bim.fdr
  Code: function(x, cross, nqtl = 1, pattern = NULL, exact = FALSE,
                 chr, ..., levels = seq(0.01, 0.99, by = 0.01), df =
                 3, qtl = bim.qtl(x, cross, nqtl, pattern, exact, ...,
                 levels = levels))
  Docs: function(x, cross, nqtl = 1, pattern = NULL, exact = FALSE,
                 chr, ..., levels = <<see below>>, df = 3, qtl = <<see
                 below>>)
plot.bim.fdr
  Code: function(x, cross, ..., fdr = bim.fdr(x, cross, ...),
                 critical.value = seq(0.05, 0.25, by = 0.05), hpd =
                 NULL)
  Docs: function(x, cross, ..., fdr = <<see below>>, critical.value =
                 <<see below>>, hpd = NULL)

Codoc mismatches from documentation object 'bim.':
plot.bim.qtl
  Code: function(x, cross = bim.cross(x), nqtl = 1, pattern = NULL,
                 exact = FALSE, chr, bw = 2, qtl = bim.qtl(x, cross,
                 nqtl, pattern, exact, , bw), level = 0.8, col =
                 "black", add = FALSE, ...)
  Docs: function(x, cross, nqtl = 1, pattern = NULL, exact = FALSE,
                 chr, bw = 2, qtl = <<see below>>, level = 0.8, col =
                 "black", add = FALSE, ...)

Codoc mismatches from documentation object 'plot.bim.diag':
plot.bim.diag
  Code: function(x, nqtl = 1, pattern = NULL, exact = FALSE, items =
                 names(x$iter)[-(1:2)], mains = items, mfrow =
                 c(nhist, 2), ...)
  Docs: function(x, nqtl = 1, pattern = NULL, exact = FALSE, items =
                 <<see below>>, mains = items, mfrow = <<see below>>,
                 ...)

Codoc mismatches from documentation object 'plot.bim.mcmc':
plot.bim.mcmc
  Code: function(x, element = c("burnin", "iter"), xlab = c("burnin
                 sequence", "mcmc sequence"), items =
                 names(x$iter)[-1], ylabs = items, types = c("b",
                 rep("l", length(items) - 1)), ...)
  Docs: function(x, element = c("burnin", "iter"), xlab = c("burnin
                 sequence", "mcmc sequence"), items = <<see below>>,
                 ylabs = items, types = <<see below>>, ...)

Codoc mismatches from documentation object 'plot.bim.model':
plot.bim.model
  Code: function(x, cross = bim.cross(x), nqtl = 1, pattern = NULL,
                 exact = FALSE, cutoff = 1, assess = bim.model(x,
                 cross, nqtl, pattern, exact, cutoff), ...)
  Docs: function(x, cross = NULL, nqtl = 1, pattern = NULL, exact =
                 FALSE, cutoff = 1, assess = <<see below>>, ...)

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'bim.effects':
  prefix

Functions with \usage entries need to have the appropriate \alias entries,
and all their arguments documented.
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* creating bim-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating bim-manual.tex ... OK
* checking bim-manual.tex ... OK