Package: oligoClasses

Version: 1.16.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.16.0.tar.gz

StartedAt: 2012-01-09 04:33:29 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:35:30 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 120.9 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/oligoClasses.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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	0.23	0.00	0.24
AssayData-methods	0.59	0.00	0.59
CNSet-class	9.27	0.06	9.42
CopyNumberSet-class	0.03	0.00	0.03
FeatureSetExtensions-class	0.68	0.00	0.69
PDInfo-methods	0.68	0.08	0.75
RangedDataCNV-classes	0	0	0
RangedDataCNV-utils	0.95	0.00	0.95
SnpSet-methods	0.08	0.00	0.08
SnpSuperSet-class	0.20	0.00	0.21
addFeatureAnnotation	4.41	0.07	4.61
affyPlatforms	0	0	0
batch	0.73	0.03	0.76
celfileDate	0.03	0.00	0.20
checkExists	0.00	0.02	0.02
checkOrder	0.11	0.00	0.11
chromosome2integer	0	0	0
data-efsExample	0	0	0
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0.00	0.01	0.01
db	0	0	0
ff_matrix	0	0	0
fileConnections	0	0	0
findOverlaps	0.74	0.02	0.78
flags	0.28	0.00	0.28
getBar	0	0	0
i2p_p2i	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.10	0.00	0.09
largeObjects	0	0	0
ldOpts	0	0	0
list.celfiles	0.02	0.00	0.03
locusLevelData	0.09	0.00	0.09
oligoSetExample	0.08	0.00	0.08
order	0.08	0.00	0.08
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0