Package: oligoClasses

Version: 1.16.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.16.0.tar.gz

StartedAt: 2012-03-24 01:45:31 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:47:51 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 139.6 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/oligoClasses.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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	0.388	0.000	0.389
AssayData-methods	0.688	0.024	0.712
CNSet-class	11.805	0.200	12.131
CopyNumberSet-class	0.044	0.000	0.048
FeatureSetExtensions-class	0.380	0.036	0.434
PDInfo-methods	0.888	0.020	0.933
RangedDataCNV-classes	0.000	0.000	0.001
RangedDataCNV-utils	1.344	0.000	1.389
SnpSet-methods	0.092	0.000	0.101
SnpSuperSet-class	0.276	0.000	0.277
addFeatureAnnotation	4.316	0.084	4.637
affyPlatforms	0.000	0.000	0.001
batch	1.020	0.008	1.038
celfileDate	0.028	0.000	0.027
checkExists	0.008	0.000	0.006
checkOrder	0.092	0.000	0.095
chromosome2integer	0	0	0
data-efsExample	0.004	0.000	0.002
data-scqsExample	0.000	0.000	0.002
data-sfsExample	0.004	0.000	0.002
data-sqsExample	0.004	0.000	0.002
db	0	0	0
ff_matrix	0	0	0
fileConnections	0	0	0
findOverlaps	0.824	0.016	0.890
flags	0.316	0.012	0.327
getBar	0	0	0
i2p_p2i	0.000	0.000	0.001
is.ffmatrix	0.000	0.004	0.001
isPackageLoaded	0.000	0.000	0.001
kind	0.064	0.020	0.083
largeObjects	0	0	0
ldOpts	0.000	0.000	0.001
list.celfiles	0.028	0.000	0.037
locusLevelData	0.064	0.004	0.068
oligoSetExample	0.056	0.000	0.055
order	0.060	0.004	0.068
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0.000	0.000	0.002