Package: oligoClasses

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.10.0.tar.gz

StartedAt: 2010-10-04 17:59:51 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:02:05 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 134.4 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/oligoClasses.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligoClasses' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
createFF: no visible global function definition for ‘ff’
delCluster: no visible global function definition for ‘stopCluster’
initializeBigMatrix: no visible binding for global variable ‘ffdf’
initializeBigVector: no visible global function definition for ‘ff’
ocLapply: no visible global function definition for ‘parLapply’
requireClusterPkg: no visible global function definition for
  ‘clusterCall’
setCluster: no visible global function definition for ‘makeCluster’
splitIndicesByNode: no visible global function definition for
  ‘clusterSplit’
getA,AlleleSet: no visible global function definition for ‘ff’
getM,AlleleSet: no visible global function definition for ‘ff’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

in method for ‘annotatedDataFrameFrom’ with signature ‘"ff_matrix"’: no definition for class "ff_matrix"
Creating a new generic function for "close" in "oligoClasses"
Creating a new generic function for "open" in "oligoClasses"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.10.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================

* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.003	0.001	0.004
CNSet-class	0.000	0.001	0.001
FeatureSetExtensions-class	0.661	0.004	0.669
PDInfo-methods	0.819	0.039	0.865
SnpSet-methods	0.105	0.001	0.106
SnpSuperSet-class	0.003	0.000	0.003
addFeatureAnnotation	18.055	0.362	18.651
affyPlatforms	0.001	0.001	0.001
celfileDate	0.047	0.006	0.085
chromosome2integer	0.000	0.000	0.001
data-efsExample	0.004	0.001	0.005
data-scqsExample	0.002	0.001	0.003
data-sfsExample	0.003	0.001	0.003
data-sqsExample	0.002	0.001	0.003
db	0.000	0.000	0.001
getBar	0.001	0.000	0.001
is.ffmatrix	0.001	0.000	0.002
isPackageLoaded	0.001	0.001	0.001
kind	0.183	0.016	0.200
largeObjects	0.001	0.000	0.002
ldOpts	0.003	0.000	0.003
list.celfiles	0.043	0.005	0.065
pdPkgFromBioC	0.000	0.000	0.001
requireAnnotation	0.000	0.000	0.001
splitVec	0.002	0.001	0.004