* using log directory 'd:/Rcompile/CRANpkg/local/3.3/mlDNA.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 'mlDNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mlDNA' version '1.1'
* 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 'mlDNA' 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
'library' or 'require' calls in package code:
  'cairoDevice' 'gplots'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.DNA.connectivitylist : .fun_conn_idx: no visible global function
  definition for 'attach.big.matrix'
.DNA.distance: no visible global function definition for
  'as.big.matrix'
.checkadjmatrix: no visible global function definition for
  'is.big.matrix'
.cor.threshold: no visible global function definition for 'qt'
.cv: no visible global function definition for 'sd'
.filterLowCorrelation: no visible global function definition for
  'is.big.matrix'
.network.differences : .fun_distance: no visible global function
  definition for 'attach.big.matrix'
.plotLines: no visible global function definition for 'lines'
.plotLines: no visible global function definition for 'legend'
.uniqueTissues: no visible binding for global variable 'tail'
.uniqueTissues: no visible global function definition for 'str_sub'
PSOL_NegativeExpansion: no visible global function definition for
  'write.table'
PSOL_NegativeExpansion: no visible global function definition for
  'install.packages'
PSOL_NegativeExpansion: no visible global function definition for 'pdf'
PSOL_NegativeExpansion: no visible global function definition for 'par'
PSOL_NegativeExpansion: no visible global function definition for
  'points'
PSOL_NegativeExpansion: no visible global function definition for
  'axis'
PSOL_NegativeExpansion: no visible global function definition for
  'mtext'
PSOL_NegativeExpansion: no visible global function definition for
  'dev.off'
PSOL_ResultExtraction: no visible global function definition for
  'read.table'
geneRanker: no visible global function definition for 'RankingTstat'
geneRanker: no visible global function definition for 'RankingFC'
geneRanker: no visible global function definition for 'RankingWilcoxon'
geneRanker: no visible global function definition for
  'RankingBaldiLong'
geneRanker: no visible global function definition for
  'RankingShrinkageT'
geneRanker: no visible global function definition for 'RankingSam'
geneRanker: no visible global function definition for
  'RankingSoftthresholdT'
geneRanker: no visible global function definition for 'RankingLimma'
geneRanker: no visible global function definition for 'toplist'
optimalScore: no visible global function definition for 'abline'
plotROC: no visible global function definition for 'par'
predictor: no visible global function definition for 'predict'
Undefined global functions or variables:
  RankingBaldiLong RankingFC RankingLimma RankingSam RankingShrinkageT
  RankingSoftthresholdT RankingTstat RankingWilcoxon abline
  as.big.matrix attach.big.matrix axis dev.off install.packages
  is.big.matrix legend lines mtext par pdf points predict qt read.table
  sd str_sub tail toplist write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "points")
  importFrom("stats", "predict", "qt", "sd")
  importFrom("utils", "install.packages", "read.table", "tail",
             "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 examples ... [6s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs