* using log directory 'd:/Rcompile/CRANpkg/local/3.3/samr.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 'samr/DESCRIPTION' ... OK
* this is package 'samr' version '2.0'
* 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 'samr' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'impute' 'matrixStats'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'impute' 'matrixStats'
  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
.error.trace: no visible global function definition for 'winDialog'
est.s0: no visible global function definition for 'quantile'
est.s0: no visible global function definition for 'mad'
est.s0: no visible global function definition for 'var'
foldchange.seq.twoclass.paired: no visible global function definition
  for 'rowMedians'
foldchange.seq.twoclass.unpaired: no visible global function definition
  for 'rowMedians'
localfdr: no visible global function definition for 'median'
localfdr: no visible global function definition for 'smooth.spline'
paired.ttest.func: no visible global function definition for 'var'
patterndiscovery.func: no visible global function definition for
  'quantile'
patterndiscovery.func: no visible global function definition for
  'median'
permute.rows: no visible global function definition for 'runif'
predictlocalfdr: no visible global function definition for 'predict'
resample: no visible global function definition for 'rpois'
resample: no visible global function definition for 'runif'
samr: no visible global function definition for 'impute.knn'
samr: no visible binding for global variable 'median'
samr: no visible global function definition for 'quantile'
samr.assess.samplesize: no visible global function definition for
  'quantile'
samr.assess.samplesize: no visible global function definition for
  'median'
samr.assess.samplesize.plot: no visible global function definition for
  'win.metafile'
samr.assess.samplesize.plot: no visible global function definition for
  'par'
samr.assess.samplesize.plot: no visible global function definition for
  'plot'
samr.assess.samplesize.plot: no visible global function definition for
  'lines'
samr.assess.samplesize.plot: no visible global function definition for
  'mtext'
samr.assess.samplesize.plot: no visible global function definition for
  'abline'
samr.assess.samplesize.plot: no visible global function definition for
  'title'
samr.assess.samplesize.plot: no visible global function definition for
  'dev.off'
samr.compute.delta.table.array: no visible binding for global variable
  'var'
samr.compute.delta.table.array: no visible binding for global variable
  'median'
samr.compute.delta.table.array: no visible binding for global variable
  'quantile'
samr.compute.delta.table.seq: no visible binding for global variable
  'median'
samr.compute.delta.table.seq: no visible binding for global variable
  'quantile'
samr.estimate.depth: no visible global function definition for
  'quantile'
samr.missrate: no visible global function definition for 'quantile'
samr.plot: no visible global function definition for 'plot'
samr.plot: no visible global function definition for 'points'
samr.plot: no visible global function definition for 'abline'
samr.tail.strength: no visible global function definition for 'var'
samr.xl.compute.plot.xy: no visible global function definition for
  'points'
samr.xl.compute.plot.xy: no visible global function definition for
  'abline'
samr.xl.error.trace: no visible global function definition for
  'winDialog'
samr.xl.impute.data: no visible global function definition for
  'impute.knn'
samr.xl.impute.data: no visible binding for global variable
  'samr.xl.var.knn.neighbors'
Undefined global functions or variables:
  abline dev.off impute.knn lines mad median mtext par plot points
  predict quantile rowMedians rpois runif samr.xl.var.knn.neighbors
  smooth.spline title var win.metafile winDialog
Consider adding
  importFrom("grDevices", "dev.off", "win.metafile")
  importFrom("graphics", "abline", "lines", "mtext", "par", "plot",
             "points", "title")
  importFrom("stats", "mad", "median", "predict", "quantile", "rpois",
             "runif", "smooth.spline", "var")
  importFrom("utils", "winDialog")
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 ... NOTE
S3 methods shown with full name in documentation object 'samr-internal':
  'plot.SAMoutput' 'print.SAMoutput'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ...
** running examples for arch 'i386' ... [26s] OK
** running examples for arch 'x64' ... [26s] OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs