* using log directory 'd:/Rcompile/CRANpkg/local/3.3/qtlhot.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'qtlhot/DESCRIPTION' ... OK
* this is package 'qtlhot' version '0.9.0'
* 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 'qtlhot' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CMSTtests : CreateDesignMatrix: no visible global function definition
  for 'model.matrix'
CMSTtests : CreateDesignMatrix: no visible global function definition
  for 'as.formula'
CMSTtests : ParametricIUCMST: no visible global function definition for
  'pnorm'
CMSTtests : NonparametricIUCMST: no visible global function definition
  for 'pbinom'
CMSTtests : GetLogLik: no visible global function definition for
  'dnorm'
CMSTtests: no visible global function definition for 'cov'
CMSTtests: no visible global function definition for 'cov2cor'
CitTests: no visible global function definition for 'lm'
CitTests: no visible global function definition for 'anova'
CitTests: no visible global function definition for 'resid'
CitTests: no visible global function definition for 'runif'
CitTests: no visible global function definition for 'pf'
CitTests: no visible global function definition for 'qnorm'
CitTests: no visible global function definition for 'pnorm'
CitTests: no visible global function definition for 'sd'
DropMissing: no visible global function definition for 'na.omit'
FDRplot: no visible global function definition for 'par'
FDRplot: no visible global function definition for 'plot'
FDRplot: no visible global function definition for 'abline'
FDRplot: no visible global function definition for 'points'
GetCommonQtls : CreateCovMatrix: no visible global function definition
  for 'formula'
GetCommonQtls : CreateCovMatrix: no visible global function definition
  for 'model.matrix'
MyMultipleTestingSim: no visible global function definition for 'runif'
MyMultipleTestingSim2: no visible global function definition for
  'runif'
SimCross1: no visible global function definition for 'rnorm'
SimCross2: no visible global function definition for 'rnorm'
SimCross3: no visible global function definition for 'rnorm'
SimCross4: no visible global function definition for 'rnorm'
SimCross5: no visible global function definition for 'rnorm'
SimCross6: no visible global function definition for 'rnorm'
SimCrossCausal: no visible global function definition for 'rnorm'
SimCrossIndep: no visible global function definition for 'rnorm'
add.rug: no visible global function definition for 'par'
add.rug: no visible global function definition for 'rug'
add.rug: no visible global function definition for 'abline'
add.rug: no visible global function definition for 'axis'
add.rug: no visible global function definition for 'mtext'
add.rug: no visible global function definition for 'title'
big.phase2: no visible binding for global variable 'window'
get.chr.pos: no visible global function definition for 'rnorm'
include.hotspots : update.pheno: no visible global function definition
  for 'rnorm'
include.hotspots : update.pheno: no visible global function definition
  for 'runif'
make.maxlod : tmpfn2: no visible global function definition for
  'median'
myapprox: no visible global function definition for 'approx'
normal.trans: no visible global function definition for 'qnorm'
p.adjust.np: no visible global function definition for 'p.adjust'
parallel.error: no visible global function definition for 'write.table'
parallel.message: no visible global function definition for
  'write.table'
plot.bic.aic: no visible global function definition for 'par'
plot.bic.aic: no visible global function definition for 'plot'
plot.bic.aic: no visible global function definition for 'abline'
plot.bic.aic: no visible global function definition for 'points'
plot.cit: no visible global function definition for 'par'
plot.cit: no visible global function definition for 'plot'
plot.cit: no visible global function definition for 'abline'
plot.cit: no visible global function definition for 'points'
plot.highlod: no visible global function definition for 'plot'
plot.hotperm : tmp.plot: no visible global function definition for
  'plot'
plot.hotperm : tmp.plot: no visible global function definition for
  'mtext'
plot.hotperm : tmp.plot: no visible global function definition for
  'abline'
plot.hotperm : tmp.plot: no visible global function definition for
  'lines'
plot.hotperm : tmp.plot: no visible global function definition for
  'text'
plot.hotperm : tmp.plot: no visible global function definition for
  'par'
plot.hotperm: no visible global function definition for 'par'
plot.hotperm: no visible global function definition for 'plot'
plot.hotperm: no visible global function definition for 'abline'
plot.hotperm: no visible global function definition for 'mtext'
plot.hotperm: no visible global function definition for 'lines'
plot.hotperm: no visible global function definition for 'text'
plot.hotperm: no visible global function definition for 'title'
plot.hotsize: no visible global function definition for 'plot'
plot.hotsize: no visible global function definition for 'abline'
plot.hotsize: no visible global function definition for 'axis'
plot.hotsize: no visible global function definition for 'mtext'
plot.non.par.cmst: no visible global function definition for 'par'
plot.non.par.cmst: no visible global function definition for 'plot'
plot.non.par.cmst: no visible global function definition for 'abline'
plot.non.par.cmst: no visible global function definition for 'points'
plot.par.cmst: no visible global function definition for 'par'
plot.par.cmst: no visible global function definition for 'plot'
plot.par.cmst: no visible global function definition for 'abline'
plot.par.cmst: no visible global function definition for 'points'
plot.par.cmst.joint: no visible global function definition for 'par'
plot.par.cmst.joint: no visible global function definition for 'plot'
plot.par.cmst.joint: no visible global function definition for 'abline'
plot.par.cmst.joint: no visible global function definition for 'points'
qtlhot.phase1: no visible global function definition for 'write.table'
sexbatch.covar: no visible global function definition for 'formula'
sexbatch.covar: no visible global function definition for
  'model.matrix'
sim.null.pheno.data: no visible global function definition for 'rnorm'
sliding.bar.plot : create.rug: no visible global function definition
  for 'median'
sliding.bar.plot: no visible global function definition for 'par'
sliding.bar.plot: no visible global function definition for 'plot'
sliding.bar.plot: no visible global function definition for 'rug'
sliding.bar.plot: no visible global function definition for 'axis'
sliding.bar.plot: no visible global function definition for 'mtext'
sliding.bar.plot: no visible global function definition for 'segments'
slidingbar.plot: no visible global function definition for 'image'
slidingbar.plot: no visible global function definition for 'mtext'
slidingbar.plot: no visible global function definition for 'abline'
slidingbar.plot: no visible global function definition for 'par'
slidingbar.plot: no visible global function definition for 'axis'
Undefined global functions or variables:
  abline anova approx as.formula axis cov cov2cor dnorm formula image
  lines lm median model.matrix mtext na.omit p.adjust par pbinom pf
  plot pnorm points qnorm resid rnorm rug runif sd segments text title
  window write.table
Consider adding
  importFrom("graphics", "abline", "axis", "image", "lines", "mtext",
             "par", "plot", "points", "rug", "segments", "text", "title")
  importFrom("stats", "anova", "approx", "as.formula", "cov", "cov2cor",
             "dnorm", "formula", "lm", "median", "model.matrix",
             "na.omit", "p.adjust", "pbinom", "pf", "pnorm", "qnorm",
             "resid", "rnorm", "runif", "sd", "window")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [7s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [15s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs