* using log directory 'd:/Rcompile/CRANpkg/local/2.15/Geneclust.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'Geneclust/DESCRIPTION' ... OK
* this is package 'Geneclust' version '1.0.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
CRAN requires a NAMESPACE file for all submissions.
* checking whether package 'Geneclust' can be installed ... WARNING
Found the following significant warnings:
  Warning: Rank mismatch in argument 'nall' at (1) (scalar and rank-1)
See 'd:/Rcompile/CRANpkg/local/2.15/Geneclust.Rcheck/00install.out' for details.
* 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
* 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 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
File 'Geneclust/R/zzz.R':
  .First.lib calls:
    cat("**********************************************************",     fill = TRUE)
    cat("*   Geneclust 1.0.1 is loaded                            *",     fill = TRUE)
    cat("*                                                        *",     fill = TRUE)
    cat("*   Use help(Geneclust) for a quick overview.            *",     fill = TRUE)
    cat("*                                                        *",     fill = TRUE)
    cat("**********************************************************",     fill = TRUE)
    require(spatial)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in ?.onAttach.

Fst: warning in matrix(nr = npopmax, nc = npopmax, 0): partial argument
  match of 'nr' to 'nrow'
Fst: warning in matrix(nr = npopmax, nc = npopmax, 0): partial argument
  match of 'nc' to 'ncol'
Fst: warning in matrix(nr = nindivtmp, nc = 2, data = -999): partial
  argument match of 'nr' to 'nrow'
Fst: warning in matrix(nr = nindivtmp, nc = 2, data = -999): partial
  argument match of 'nc' to 'ncol'
mcmcgeneclust: warning in write.table(param, file = paste(path.mcmc,
  "paraminfer.txt", sep = ""), quote = FALSE, row.name = FALSE,
  col.name = FALSE): partial argument match of 'row.name' to
  'row.names'
mcmcgeneclust: warning in write.table(param, file = paste(path.mcmc,
  "paraminfer.txt", sep = ""), quote = FALSE, row.name = FALSE,
  col.name = FALSE): partial argument match of 'col.name' to
  'col.names'
postclassif: warning in matrix(nr = nindiv, byrow = FALSE, data =
  updatelabel): partial argument match of 'nr' to 'nrow'
postclassif: warning in matrix(1:2, nr = 1, ncol = 2): partial argument
  match of 'nr' to 'nrow'
simpatch: warning in matrix(nr = nindiv, nc = nloc * 2): partial
  argument match of 'nr' to 'nrow'
simpatch: warning in matrix(nr = nindiv, nc = nloc * 2): partial
  argument match of 'nc' to 'ncol'
simpatch: warning in write.table(param, file = paste(file,
  "paramsimu.txt", sep = ""), quote = FALSE, row.name = FALSE, col.name
  = FALSE): partial argument match of 'row.name' to 'row.names'
simpatch: warning in write.table(param, file = paste(file,
  "paramsimu.txt", sep = ""), quote = FALSE, row.name = FALSE, col.name
  = FALSE): partial argument match of 'col.name' to 'col.names'
simpottsdir: warning in matrix(recup, nr = nindiv, byrow = FALSE):
  partial argument match of 'nr' to 'nrow'
* checking Rd files ... NOTE
prepare_Rd: FormatGenotypes.Rd:35: Dropping empty section \keyword
prepare_Rd: FormatGenotypes.Rd:30: Dropping empty section \seealso
prepare_Rd: Fst.Rd:36: Dropping empty section \keyword
prepare_Rd: Geneclust-package.Rd:138: Dropping empty section \keyword
prepare_Rd: Geneclust-package.Rd:141-144: Dropping empty section \examples
prepare_Rd: geneclust.Rd:176: Dropping empty section \keyword
prepare_Rd: geneclust.Rd:178-180: Dropping empty section \examples
prepare_Rd: mcmcgeneclust.Rd:116: Dropping empty section \keyword
prepare_Rd: postclassif.Rd:43: Dropping empty section \keyword
prepare_Rd: postfis.Rd:31: Dropping empty section \keyword
prepare_Rd: postpsi.Rd:24: Dropping empty section \keyword
prepare_Rd: setplot.Rd:24: Dropping empty section \keyword
prepare_Rd: simpatch.Rd:61: Dropping empty section \keyword
prepare_Rd: simpatch.Rd:57: Dropping empty section \seealso
prepare_Rd: simpottsdir.Rd:55: Dropping empty section \keyword
prepare_Rd: subsample.Rd:29: Dropping empty section \keyword
prepare_Rd: tablecst.Rd:67: Dropping empty section \keyword
* 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 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 ... NOTE
File 'd:/Rcompile/CRANpkg/lib/2.15/Geneclust/libs/i386/Geneclust.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'main.o', 'mainpotts.o'
File 'd:/Rcompile/CRANpkg/lib/2.15/Geneclust/libs/x64/Geneclust.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'main.o', 'mainpotts.o'

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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.
NOTE: There were 4 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/Geneclust.Rcheck/00check.log'
for details.