* using log directory 'd:/Rcompile/CRANpkg/local/3.3/gtx.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 'gtx/DESCRIPTION' ... OK
* this is package 'gtx' version '0.0.8'
* 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 'gtx' can be installed ... OK
* checking installed package size ... OK
* 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
* 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
Package in Depends field not imported from: 'survival'
  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
abf.normal : <anonymous>: no visible global function definition for
  'dnorm'
abf.t : <anonymous>: no visible global function definition for 'dt'
abf.t : <anonymous>: no visible global function definition for 'dnorm'
chi2ncp: no visible global function definition for 'qchisq'
chi2ncp: no visible global function definition for 'pchisq'
chi2ncp: no visible global function definition for 'uniroot'
chi2ncp : <anonymous>: no visible global function definition for
  'pchisq'
coeff.extract: no visible global function definition for 'coefficients'
contrasting.rainbow: no visible global function definition for
  'rainbow'
fitmix: no visible global function definition for 'rexp'
fitmix: no visible global function definition for 'sd'
fitmix.plot: no visible global function definition for 'density'
fitmix.plot: no visible global function definition for 'plot'
fitmix.plot: no visible global function definition for 'rug'
fitmix.plot: no visible global function definition for 'polygon'
fitmix.plot: no visible global function definition for 'lines'
fitmix.plot: no visible global function definition for 'dnorm'
fitmix.plot: no visible global function definition for 'rainbow'
fitmix.plot : <anonymous>: no visible global function definition for
  'dnorm'
fitmix.plot: no visible global function definition for 'legend'
fitmix.simulate: no visible global function definition for 'rnorm'
fitmix1: no visible global function definition for 'quantile'
fitmix1: no visible global function definition for 'sd'
fitmix1 : <anonymous>: no visible global function definition for
  'dnorm'
gls.approx.logistic: no visible global function definition for
  'as.formula'
gls.approx.logistic: no visible global function definition for
  'predict'
gls.approx.logistic: no visible global function definition for 'glm'
gls.approx.logistic: no visible binding for global variable
  'na.exclude'
grs.filter.Qrs: no visible global function definition for 'pchisq'
grs.onesnp.apply: no visible global function definition for 'update'
grs.onesnp.apply: no visible global function definition for
  'update.formula'
grs.onesnp.apply: no visible global function definition for 'formula'
grs.plot: no visible global function definition for 'plot'
grs.plot: no visible global function definition for 'qnorm'
grs.plot: no visible global function definition for 'abline'
grs.plot: no visible global function definition for 'lines'
grs.plot: no visible global function definition for 'points'
grs.summary: no visible global function definition for 'pchisq'
hapmap.read.haplotypes: no visible global function definition for
  'read.table'
hapmap.snpdata: no visible global function definition for 'na.omit'
multipheno.T2: no visible global function definition for 'cor'
multipheno.T2: no visible global function definition for 'pchisq'
read.snpdata.impute: no visible global function definition for
  'read.table'
read.snpdata.mach: no visible global function definition for
  'read.table'
read.snpdata.plink: no visible global function definition for
  'read.table'
run.blat: no visible global function definition for 'read.table'
stepdown.moments2: no visible global function definition for 'qchisq'
stepdown.moments2: no visible global function definition for 'pchisq'
stepup.moments2: no visible global function definition for 'qchisq'
stepup.moments2: no visible global function definition for 'pchisq'
test.subsample: no visible global function definition for 'update'
test.subsample: no visible global function definition for
  'update.formula'
test.subsample: no visible global function definition for 'formula'
test.subsample: no visible global function definition for 'binom.test'
Undefined global functions or variables:
  abline as.formula binom.test coefficients cor density dnorm dt
  formula glm legend lines na.exclude na.omit pchisq plot points
  polygon predict qchisq qnorm quantile rainbow read.table rexp rnorm
  rug sd uniroot update update.formula
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "polygon", "rug")
  importFrom("stats", "as.formula", "binom.test", "coefficients", "cor",
             "density", "dnorm", "dt", "formula", "glm", "na.exclude",
             "na.omit", "pchisq", "predict", "qchisq", "qnorm",
             "quantile", "rexp", "rnorm", "sd", "uniroot", "update",
             "update.formula")
  importFrom("utils", "read.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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-33\unhbox\voidb@x \penalty \@M \ {}1.
2/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs