BioC 3.2: CHECK report for vtpnet on moscato1

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### Running command:
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###   rm -rf vtpnet.buildbin-libdir vtpnet.Rcheck && mkdir vtpnet.buildbin-libdir vtpnet.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=vtpnet.buildbin-libdir vtpnet_0.10.0.tar.gz >vtpnet.Rcheck\00install.out 2>&1 && cp vtpnet.Rcheck\00install.out vtpnet-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=vtpnet.buildbin-libdir --install="check:vtpnet-install.out" --force-multiarch --no-vignettes --timings vtpnet_0.10.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/vtpnet.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'vtpnet/DESCRIPTION' ... OK
* this is package 'vtpnet' version '0.10.0'
* 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 'vtpnet' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.2Mb
  sub-directories of 1Mb or more:
    data  20.0Mb
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'doParallel' 'foreach'
  Please remove these calls from your code.
'library' or 'require' call to 'MotifDb' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'doParallel' 'foreach'
  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
rng2facHits: warning in dir(patt = "rda$"): partial argument match of
  'patt' to 'pattern'
runfimo: warning in dir(patt = "_out"): partial argument match of
  'patt' to 'pattern'
getOneHits: no visible global function definition for 'metadata<-'
gwMatchPWM: no visible binding for global variable 'Hsapiens'
gwMatchPWM: no visible global function definition for '%dopar%'
gwMatchPWM: no visible global function definition for 'foreach'
gwMatchPWM: no visible binding for global variable 'i'
gwMatchPWM: no visible global function definition for 'matchPWM'
gwMatchPWM: no visible global function definition for
  'PWMscoreStartingAt'
gwMatchPWM: no visible global function definition for 'subject'
rng2facHits: no visible global function definition for
  'registerDoParallel'
rng2facHits: no visible global function definition for '%dopar%'
rng2facHits: no visible global function definition for 'foreach'
rng2facHits: no visible binding for global variable 'i'
runfimo: no visible global function definition for '%dopar%'
runfimo: no visible global function definition for 'foreach'
runfimo: no visible binding for global variable 'i'
setupGWPM: no visible global function definition for
  'registerDoParallel'
* checking Rd files ... NOTE
prepare_Rd: vtpnet-package.Rd:48-50: Dropping empty section \references
prepare_Rd: vtpnet-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: vtpnet-package.Rd:55-56: Dropping empty section \examples
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'ShortRead'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/vtpnet.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'vtpnet' ...
** R
** data
** inst
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: replacing previous import 'ggplot2::Position' by 'S4Vectors::Position' when loading 'gwascat'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: replacing previous import 'ggplot2::Position' by 'S4Vectors::Position' when loading 'gwascat'

install for x64

* installing *source* package 'vtpnet' ...
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
Warning: replacing previous import 'ggplot2::Position' by 'S4Vectors::Position' when loading 'gwascat'
* MD5 sums
packaged installation of 'vtpnet' as vtpnet_0.10.0.zip
* DONE (vtpnet)

BioC 3.2: CHECK report for vtpnet on moscato1

Summary

Command output