BioC 2.13: CHECK report for Rmagpie on moscato1

Package: Rmagpie

Version: 1.18.0

Command: rm -rf Rmagpie.buildbin-libdir && mkdir Rmagpie.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rmagpie.buildbin-libdir Rmagpie_1.18.0.tar.gz >Rmagpie-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=Rmagpie.buildbin-libdir --install="check:Rmagpie-install.out" --force-multiarch --no-vignettes --timings Rmagpie_1.18.0.tar.gz && mv Rmagpie.buildbin-libdir/* Rmagpie.Rcheck/ && rmdir Rmagpie.buildbin-libdir

StartedAt: 2014-04-05 06:22:43 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:25:27 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 164.9 seconds

RetCode: 0

Status:  OK

CheckDir: Rmagpie.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/Rmagpie.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.18.0'
* 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 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'Magpie_examples.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [35s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
runTwoLayerExtCV-methods         12.11   0.00   12.12
plotErrorsFoldTwoLayerCV-methods  7.15   0.00    7.15
getResults-methods                5.90   0.05    5.95
** running examples for arch 'x64' ... [39s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
runTwoLayerExtCV-methods         16.42   0.00   16.41
plotErrorsFoldTwoLayerCV-methods  6.35   0.01    6.37
getResults-methods                5.82   0.00    5.81
* 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 4 notes.
See
  'D:/biocbld/bbs-2.13-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_1.18.0.zip
* DONE (Rmagpie)

name	user	system	elapsed
classifyNewSamples-methods	1.67	0.00	1.67
experiment-class	0.09	0.00	0.10
finalClassifier-class	0.12	0.01	0.14
findFinalClassifier-methods	0.17	0.02	0.19
geneSubsets-class	0.03	0.00	0.03
getDataset-methods	0.02	0.00	0.02
getFeatureSelectionOptions-methods	0.02	0.00	0.02
getFinalClassifier	0.30	0.01	0.31
getResults-methods	5.90	0.05	5.95
plotErrorsFoldTwoLayerCV-methods	7.15	0.00	7.15
plotErrorsRepeatedOneLayerCV	1.00	0.03	1.11
plotErrorsSummaryOneLayerCV-methods	1.56	0.00	1.56
rankedGenesImg-methods	0.07	0.00	0.08
runOneLayerExtCV-methods	1.23	0.00	1.23
runTwoLayerExtCV-methods	12.11	0.00	12.12
setDataset-methods	0.01	0.00	0.01
setFeatureSelectionOptions-methods	0.12	0.00	0.13
thresholds-class	0.02	0.00	0.01
vV70genes	0.02	0.00	0.02

name	user	system	elapsed
classifyNewSamples-methods	1.82	0.01	1.84
experiment-class	0.14	0.02	0.15
finalClassifier-class	0.08	0.00	0.08
findFinalClassifier-methods	0.17	0.00	0.17
geneSubsets-class	0.03	0.00	0.03
getDataset-methods	0.01	0.00	0.02
getFeatureSelectionOptions-methods	0.09	0.00	0.10
getFinalClassifier	0.24	0.00	0.23
getResults-methods	5.82	0.00	5.81
plotErrorsFoldTwoLayerCV-methods	6.35	0.01	6.37
plotErrorsRepeatedOneLayerCV	1.56	0.00	1.56
plotErrorsSummaryOneLayerCV-methods	1.9	0.0	1.9
rankedGenesImg-methods	0	0	0
runOneLayerExtCV-methods	1.56	0.00	1.56
runTwoLayerExtCV-methods	16.42	0.00	16.41
setDataset-methods	0.01	0.00	0.02
setFeatureSelectionOptions-methods	0.03	0.00	0.03
thresholds-class	0	0	0
vV70genes	0	0	0