BioC 2.12: CHECK report for virtualArray on moscato2

Package: virtualArray

Version: 1.3.1

Command: rm -rf virtualArray.buildbin-libdir && mkdir virtualArray.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=virtualArray.buildbin-libdir virtualArray_1.3.1.tar.gz >virtualArray-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=virtualArray.buildbin-libdir --install="check:virtualArray-install.out" --force-multiarch --no-vignettes --timings virtualArray_1.3.1.tar.gz && mv virtualArray.buildbin-libdir/* virtualArray.Rcheck/ && rmdir virtualArray.buildbin-libdir

StartedAt: 2013-03-25 05:16:06 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:19:38 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 211.8 seconds

RetCode: 0

Status: OK

CheckDir: virtualArray.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/virtualArray.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 '1.3.1'
* 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 ... 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
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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' ... [21s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
virtualArrayBuildfData 6.58   0.16    6.76
** running examples for arch 'x64' ... [22s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
virtualArrayBuildfData 6.74   0.31    7.07
virtualArrayBuildExprs 5.18   0.06    5.24
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.12-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 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import 'new' when loading 'methods'
Creating a generic function from function 'virtualArrayComBat' in package 'virtualArray'
** help
*** installing help indices
** building package indices
** installing vignettes
   'virtualArray.Rnw' 
** testing if installed package can be loaded
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import 'new' when loading 'methods'

install for x64

* installing *source* package 'virtualArray' ...
** testing if installed package can be loaded
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import 'new' when loading 'methods'
* MD5 sums
packaged installation of 'virtualArray' as virtualArray_1.3.1.zip
* DONE (virtualArray)

Summary

Command output