* using log directory 'd:/Rcompile/CRANpkg/local/3.4/MEET.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'MEET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEET' version '5.1.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'seqinr' 'pcaMethods' 'Matrix' 'ROCR' 'Hmisc' 'KernSmooth' 'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'MEET' 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
* 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:
  'Hmisc' 'KernSmooth' 'Matrix' 'ROCR' 'methods' 'pcaMethods' 'seqLogo'
  'seqinr'
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [21s] NOTE
DivergenceDROSOPHILA: no visible global function definition for 'data'
DivergenceHOMO: no visible global function definition for 'data'
DivergenceMUS: no visible global function definition for 'data'
DivergenceRATTUS: no visible global function definition for 'data'
EntropyDROSOPHILA: no visible global function definition for 'data'
EntropyHOMO: no visible global function definition for 'data'
EntropyMUS: no visible global function definition for 'data'
EntropyRATTUS: no visible global function definition for 'data'
JacksonParameters: no visible global function definition for 'prcomp'
MEET: no visible global function definition for 'write.table'
MEET: no visible global function definition for 'read.table'
MEET: no visible global function definition for 'data'
PCanalysis: no visible global function definition for 'residuals'
PredictPCA: no visible global function definition for 'residuals'
QresidualsDROSOPHILA: no visible global function definition for 'data'
QresidualsHOMO: no visible global function definition for 'data'
QresidualsMUS: no visible global function definition for 'data'
QresidualsRATTUS: no visible global function definition for 'data'
QtoJackson: no visible global function definition for 'pnorm'
Read.aligned: no visible global function definition for 'read.table'
chooseModel : <anonymous>: no visible global function definition for
  'sd'
pvalue: no visible global function definition for 'sd'
pvalue: no visible global function definition for 'extendrange'
writeMEME: no visible global function definition for 'write.table'
writeResultsHTML: no visible global function definition for 'data'
writeResultsHTML: no visible binding for global variable
  'RattusEntropy'
writeResultsHTML: no visible binding for global variable
  'RattusDivergence'
writeResultsHTML: no visible binding for global variable
  'RattusQresiduals'
writeResultsHTML: no visible binding for global variable 'MusEntropy'
writeResultsHTML: no visible binding for global variable
  'MusDivergence'
writeResultsHTML: no visible binding for global variable
  'MusQresiduals'
writeResultsHTML: no visible binding for global variable
  'DrosophilaEntropy'
writeResultsHTML: no visible binding for global variable
  'DrosophilaDivergence'
writeResultsHTML: no visible binding for global variable
  'DrosophilaQresiduals'
writeResultsHTML: no visible binding for global variable 'HomoEntropy'
writeResultsHTML: no visible binding for global variable
  'HomoDivergence'
writeResultsHTML: no visible binding for global variable
  'HomoQresiduals'
writeResultsHTML: no visible global function definition for 'png'
writeResultsHTML: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  DrosophilaDivergence DrosophilaEntropy DrosophilaQresiduals
  HomoDivergence HomoEntropy HomoQresiduals MusDivergence MusEntropy
  MusQresiduals RattusDivergence RattusEntropy RattusQresiduals data
  dev.off extendrange png pnorm prcomp read.table residuals sd
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "extendrange", "png")
  importFrom("stats", "pnorm", "prcomp", "residuals", "sd")
  importFrom("utils", "data", "read.table", "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 compiled code ... OK
* checking examples ...
** running examples for arch 'i386' ... [16s] OK
** running examples for arch 'x64' ... [16s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs