* using log directory 'd:/Rcompile/CRANpkg/local/3.2/GenABEL.Rcheck'
* using R version 3.2.5 (2016-04-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'GenABEL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenABEL' version '1.8-0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenABEL' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.3Mb
* 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
* 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
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... 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 loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'DatABEL' 'genetics' 'haplo.stats' 'hglm' 'qvalue'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'GenABEL.data' 'MASS' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
arrange_probabel_phe: no visible global function definition for
  'databel'
as.genotype.snp.data: no visible global function definition for
  'genotype'
check.marker.internal: no visible global function definition for
  'qvalue'
extract.annotation.impute: no visible global function definition for
  'extract_text_file_columns'
extract.annotation.mach: no visible global function definition for
  'extract_text_file_columns'
impute2databel: no visible global function definition for
  'get_temporary_file_name'
impute2databel: no visible global function definition for
  'text2databel'
impute2databel: no visible global function definition for
  'get_dimnames'
impute2databel: no visible global function definition for 'apply2dfo'
impute2databel: no visible global function definition for 'databel'
impute2databel: no visible global function definition for
  'set_dimnames<-'
impute2databel: no visible global function definition for 'disconnect'
impute2mach: no visible global function definition for 'get_dimnames'
impute2mach: no visible global function definition for 'disconnect'
mach2databel: no visible global function definition for
  'get_temporary_file_name'
mach2databel: no visible global function definition for 'text2databel'
mach2databel: no visible global function definition for 'get_dimnames'
minimac2databel: no visible global function definition for
  'get_temporary_file_name'
minimac2databel: no visible global function definition for
  'text2databel'
minimac2databel: no visible global function definition for
  'get_dimnames'
polygenic: no visible global function definition for 'ginv'
polygenic_hglm: no visible global function definition for 'hglm'
polygenic_hglm: no visible global function definition for 'ginv'
scan.haplo: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'score.sim.control'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... NOTE
Found the following Makefile(s) without a final LF:
  inst/unitTests/Makefile
Some 'make' programs ignore lines not ending in LF.
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [74s] OK
** running examples for arch 'x64' ... [77s] OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs