Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 2.12: CHECK report for Rmagpie on petty

This page was generated on 2013-10-09 09:39:46 -0700 (Wed, 09 Oct 2013).

Package 552/671HostnameOS / ArchBUILDCHECKBUILD BIN
Rmagpie 1.16.0
Camille Maumet
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Rmagpie
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: Rmagpie
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rmagpie_1.16.0.tar.gz
StartedAt: 2013-10-08 23:43:07 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:46:10 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 183.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Rmagpie.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Rmagpie.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'Rmagpie' can be installed ... [11s/12s] 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
* 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 sizes of PDF files under 'inst/doc' ... 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 ... [58s/59s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
runTwoLayerExtCV-methods         20.657  0.089  21.090
plotErrorsFoldTwoLayerCV-methods 11.240  0.033  11.480
getResults-methods               10.377  0.152  10.669
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/Rmagpie.Rcheck/00check.log'
for details.

Rmagpie.Rcheck/00install.out:

* 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
* DONE (Rmagpie)

Rmagpie.Rcheck/Rmagpie-Ex.timings:

nameusersystemelapsed
classifyNewSamples-methods3.5220.0743.614
experiment-class0.1350.0060.141
finalClassifier-class0.1640.0030.168
findFinalClassifier-methods0.3060.0130.321
geneSubsets-class0.1630.0040.167
getDataset-methods0.0320.0040.035
getFeatureSelectionOptions-methods0.0500.0030.054
getFinalClassifier0.3500.1060.459
getResults-methods10.377 0.15210.669
plotErrorsFoldTwoLayerCV-methods11.240 0.03311.480
plotErrorsRepeatedOneLayerCV2.0810.0102.102
plotErrorsSummaryOneLayerCV-methods2.0940.0152.143
rankedGenesImg-methods0.0160.0010.016
runOneLayerExtCV-methods1.7890.0091.812
runTwoLayerExtCV-methods20.657 0.08921.090
setDataset-methods0.0310.0020.036
setFeatureSelectionOptions-methods0.0610.0030.065
thresholds-class0.0220.0020.025
vV70genes0.0160.0020.025