BioC 2.12: CHECK report for Rmagpie on moscato2

Package: Rmagpie

Version: 1.16.0

Command: rm -rf Rmagpie.buildbin-libdir && mkdir Rmagpie.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.16.0.tar.gz >Rmagpie-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.16.0.tar.gz && mv Rmagpie.buildbin-libdir/* Rmagpie.Rcheck/ && rmdir Rmagpie.buildbin-libdir

StartedAt: 2013-10-09 03:56:55 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:00:23 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 207.5 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/Rmagpie.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rmagpie/DESCRIPTION' ... OK
* this is package 'Rmagpie' version '1.16.0'
* 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 'Rmagpie' 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
twoLayerExtCV: warning in performAValidation(data = eset, trainIndices
  = extInds[[i]], noGenes = upToBestSelectedFeature, classes = classes,
  classifierName = classifierName, verbose = verbose, kernel = kernel,
  featureSelectionFun = featureSelectionFun, trainTestFun =
  trainTestFun): partial argument match of 'data' to 'dataset'
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for 'getNoOfOptions<-'
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for 'getNoModels<-'
* 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'fancyvrb.sty'

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' ... [46s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
runTwoLayerExtCV-methods         14.54      0   14.54
plotErrorsFoldTwoLayerCV-methods  9.05      0    9.05
getResults-methods                8.82      0    9.02
** running examples for arch 'x64' ... [46s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
runTwoLayerExtCV-methods         15.59   0.00   15.59
getResults-methods               10.19   0.02   10.21
plotErrorsFoldTwoLayerCV-methods  9.52   0.00    9.51
* 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 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/Rmagpie.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Rmagpie' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Rmagpie' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rmagpie' as Rmagpie_1.16.0.zip
* DONE (Rmagpie)