Package: oligoClasses

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.16.0.tar.gz

StartedAt: 2012-03-24 02:54:08 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:57:07 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 179.3 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/oligoClasses.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.16.0'
* 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 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 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
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'
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'
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: CNSet-class.Rd:107: Dropping empty section \seealso
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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  ================================================================================
  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
Creating a generic function for 'open' from package 'base' in package 'oligoClasses'
Creating a generic function for 'close' from package 'base' in package 'oligoClasses'
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
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	0.339	0.007	0.362
AssayData-methods	0.756	0.039	0.874
CNSet-class	11.523	0.283	12.384
CopyNumberSet-class	0.060	0.001	0.064
FeatureSetExtensions-class	0.796	0.013	0.830
PDInfo-methods	1.049	0.063	1.115
RangedDataCNV-classes	0.002	0.000	0.002
RangedDataCNV-utils	1.184	0.004	1.192
SnpSet-methods	0.166	0.009	0.176
SnpSuperSet-class	0.281	0.004	0.287
addFeatureAnnotation	6.141	0.166	6.660
affyPlatforms	0.001	0.000	0.002
batch	0.980	0.034	1.127
celfileDate	0.056	0.010	0.104
checkExists	0.010	0.003	0.014
checkOrder	0.184	0.021	0.253
chromosome2integer	0.000	0.000	0.001
data-efsExample	0.003	0.001	0.003
data-scqsExample	0.003	0.001	0.008
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.002	0.001	0.003
db	0.001	0.000	0.000
ff_matrix	0.001	0.000	0.003
fileConnections	0	0	0
findOverlaps	1.125	0.045	1.244
flags	0.375	0.019	0.401
getBar	0.000	0.000	0.001
i2p_p2i	0.001	0.000	0.001
is.ffmatrix	0.001	0.000	0.000
isPackageLoaded	0.000	0.001	0.001
kind	0.177	0.011	0.189
largeObjects	0.001	0.000	0.001
ldOpts	0.002	0.000	0.002
list.celfiles	0.046	0.005	0.051
locusLevelData	0.134	0.013	0.147
oligoSetExample	0.118	0.006	0.125
order	0.144	0.011	0.157
pdPkgFromBioC	0.000	0.000	0.001
requireAnnotation	0	0	0
splitVec	0.002	0.002	0.003