Package: oligoClasses

Version: 1.13.18

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.13.18.tar.gz

StartedAt: 2011-03-17 16:59:59 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:02:02 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 123.5 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/oligoClasses.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.13.18'
* 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 installed package size ... 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'
featureDataFrom: no visible binding for global variable 'cdfName'
initializeBigMatrix: no visible binding for global variable 'ffdf'
initializeBigVector: no visible global function definition for 'ff'
initializeLMObject: no visible global function definition for
  'paramNames'
initializeLMObject: no visible binding for global variable 'ffdf'
ocLapply: no visible global function definition for 'parLapply'
ocProbesets: no visible global function definition for 'clusterCall'
ocSamples: no visible global function definition for 'clusterCall'
relocateObject : f2: no visible global function definition for
  'physical<-'
relocateObject: no visible global function definition for 'physical<-'
relocateObject : relocate.fxn: no visible binding for global variable
  'nmm'
relocateObject : relocate.fxn: no visible global function definition
  for 'filename<-'
relocateObject : relocate.fxn: no visible global function definition
  for 'physical<-'
requireClusterPkg: no visible global function definition for
  'clusterCall'
setCluster: no visible global function definition for 'makeCluster'
splitIndicesByNode: no visible global function definition for
  'clusterSplit'
* checking Rd files ... NOTE
prepare_Rd: batch.Rd:44-46: Dropping empty section \details
* 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 ... NOTE
'library' or 'require' calls not declared from:
  hapmapsnp5 hapmapsnp6
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  ================================================================================
  Welcome to oligoClasses version 1.13.18
  ================================================================================
  Large dataset support for 'oligo/crlmm': Disabled
       - Load 'ff'
  ================================================================================
  Parallel computing support for 'oligo/crlmm': Disabled
       - Load 'ff'
       - Load 'snow'
       - Use options(cluster=makeCluster(...))
  ================================================================================
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

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

Welcome to Bioconductor

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

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 1.13.18
================================================================================
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	0.263	0.003	0.266
AssayData-methods	0.653	0.015	0.668
CNSet-class	7.725	0.109	7.867
FeatureSetExtensions-class	0.574	0.011	0.586
PDInfo-methods	0.552	0.023	0.575
SnpSet-methods	0.253	0.009	0.307
SnpSuperSet-class	0.210	0.002	0.211
addFeatureAnnotation	3.648	0.048	3.782
affyPlatforms	0.001	0.000	0.001
batch	0.675	0.013	0.689
celfileDate	0.033	0.003	0.069
checkExists	0.008	0.001	0.009
chromosome2integer	0.001	0.001	0.000
data-efsExample	0.002	0.000	0.004
data-scqsExample	0.002	0.000	0.002
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.002	0.001	0.002
db	0.001	0.000	0.001
ff_matrix	0.001	0.000	0.001
flags	0.312	0.014	0.326
getBar	0.001	0.001	0.000
i2p_p2i	0.000	0.000	0.001
is.ffmatrix	0	0	0
isPackageLoaded	0.000	0.001	0.001
kind	0.127	0.007	0.134
largeObjects	0.001	0.000	0.001
ldOpts	0.002	0.000	0.002
list.celfiles	0.028	0.002	0.056
pdPkgFromBioC	0.001	0.000	0.000
relocateObject	0.001	0.000	0.001
requireAnnotation	0	0	0
splitVec	0.002	0.001	0.002