BioC 2.13: CHECK report for virtualArray on moscato1

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/virtualArray.Rcheck'
* using R version 3.0.2 (2013-09-25)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'virtualArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'virtualArray' version '1.6.0'
* package encoding: latin1
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'virtualArray' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'plyr' 'preprocessCore'
  These packages needs to imported from for the case when
  this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
File 'virtualArray/R/onLoad.R':
  .onLoad calls:
    message("To support our work please cite:")
    print(citation("virtualArray"))
    message("Thanks.")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

nordi1p_getoutliers: no visible global function definition for
  'rm.outlier'
virtualArrayBuildfData: no visible global function definition for
  'biocinstallRepos'
virtualArrayExpressionSets: no visible global function definition for
  'biocinstallRepos'
virtualArrayExpressionSets: no visible global function definition for
  'register'
virtualArrayExpressionSets: no visible global function definition for
  'MulticoreParam'
virtualArrayExpressionSets: no visible binding for global variable
  'bplapply'
virtualArrayLoadRaw: no visible binding for global variable
  'rawdata_U133Plus2'
virtualArrayLoadRaw: no visible binding for global variable
  'rawdata_U219'
virtualArrayLoadRaw: no visible binding for global variable
  'rawdata_U133A'
virtualArrayComBat,data.frame: no visible global function definition
  for 'as.data.matrix'
* checking Rd files ... NOTE
prepare_Rd: normalize.ExpressionSet.gq.Rd:41-43: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.mc.Rd:40-42: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.mrs.Rd:40-42: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.nordi.Rd:42-44: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.qd.Rd:39-41: Dropping empty section \note
* 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' ... NOTE
The following files should probably not be installed:
  'virtualArray-016.pdf'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [30s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
virtualArrayBuildfData 6.61   0.34    6.96
virtualArrayBuildExprs 5.44   0.01    5.46
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
virtualArrayBuildfData 6.94   0.28    7.28
virtualArrayBuildExprs 5.85   0.11    5.96
* checking for unstated dependencies in vignettes ... OK
* 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

NOTE: There were 6 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/virtualArray.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'virtualArray' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import by 'methods::new' when loading 'virtualArray'
Warning: replacing previous import by 'stats::density' when loading 'virtualArray'
Warning: replacing previous import by 'utils::installed.packages' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.csv' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.table' when loading 'virtualArray'
Warning: replacing previous import by 'utils::write.table' when loading 'virtualArray'
Creating a generic function from function 'virtualArrayComBat' in package 'virtualArray'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import by 'methods::new' when loading 'virtualArray'
Warning: replacing previous import by 'stats::density' when loading 'virtualArray'
Warning: replacing previous import by 'utils::installed.packages' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.csv' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.table' when loading 'virtualArray'
Warning: replacing previous import by 'utils::write.table' when loading 'virtualArray'
To support our work please cite:

To cite package 'virtualArray' in publications use:

  Andreas Heider and Rüdiger Alt (2013). virtualArray: a R/bioconductor
  package to merge raw data from different microarray platforms. R
  package version 1.6.0.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {virtualArray: a R/bioconductor package to merge raw data from different microarray platforms},
    author = {{Andreas Heider} and {Rüdiger Alt}},
    year = {2013},
    note = {R package version 1.6.0},
    journal = {BMC Bioinformatics},
    volume = {14},
    pages = {75},
  }

Thanks.

install for x64

* installing *source* package 'virtualArray' ...
** testing if installed package can be loaded
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import by 'methods::new' when loading 'virtualArray'
Warning: replacing previous import by 'stats::density' when loading 'virtualArray'
Warning: replacing previous import by 'utils::installed.packages' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.csv' when loading 'virtualArray'
Warning: replacing previous import by 'utils::read.table' when loading 'virtualArray'
Warning: replacing previous import by 'utils::write.table' when loading 'virtualArray'
To support our work please cite:

To cite package 'virtualArray' in publications use:

  Andreas Heider and Rüdiger Alt (2013). virtualArray: a R/bioconductor
  package to merge raw data from different microarray platforms. R
  package version 1.6.0.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {virtualArray: a R/bioconductor package to merge raw data from different microarray platforms},
    author = {{Andreas Heider} and {Rüdiger Alt}},
    year = {2013},
    note = {R package version 1.6.0},
    journal = {BMC Bioinformatics},
    volume = {14},
    pages = {75},
  }

Thanks.
* MD5 sums
packaged installation of 'virtualArray' as virtualArray_1.6.0.zip
* DONE (virtualArray)

BioC 2.13: CHECK report for virtualArray on moscato1

Summary

Command output