Package: oligoClasses

Version: 1.12.2

Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings oligoClasses_1.12.2.tar.gz

StartedAt: 2011-03-31 09:36:14 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 09:39:07 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 172.5 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/oligoClasses.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.12.2'
* 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 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'
requireClusterPkg: no visible global function definition for
  'clusterCall'
setCluster: no visible global function definition for 'makeCluster'
splitIndicesByNode: no visible global function definition for
  'clusterSplit'
coerce,CNSet-CopyNumberSet: no visible global function definition for
  'totalCopynumber'
coerce,CNSet-oligoSnpSet: no visible global function definition for
  'totalCopynumber'
coerce,CNSetLM-CNSet: no visible global function definition for
  'physical'
getA,AlleleSet: no visible global function definition for 'ff'
getM,AlleleSet: no visible global function definition for 'ff'
updateObject,CNSet: no visible binding for global variable '....'
* checking Rd files ... NOTE
prepare_Rd: CNSet-class.Rd:105-106: 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 ... NOTE
'library' or 'require' calls not declared from:
  hapmapsnp5 hapmapsnp6
* checking data for non-ASCII characters ... NOTE
  ================================================================================
  Welcome to oligoClasses version 1.12.2
  ================================================================================
  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 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
  'openVignette()'. 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 1.12.2
================================================================================
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	0.28	0.00	0.28
AssayData-methods	0.68	0.00	0.68
CNSet-class	8.56	0.05	8.78
FeatureSetExtensions-class	0.35	0.00	0.35
PDInfo-methods	0.47	0.06	0.53
SnpSet-methods	0.46	0.02	0.60
SnpSuperSet-class	0.10	0.00	0.11
addFeatureAnnotation	3.88	0.05	4.01
affyPlatforms	0	0	0
batch	0.41	0.01	0.42
celfileDate	0.02	0.00	0.34
checkExists	0.00	0.00	0.08
chromosome2integer	0	0	0
data-efsExample	0.00	0.02	0.02
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0	0	0
db	0	0	0
ff_matrix	0	0	0
flags	0.17	0.01	0.19
getBar	0	0	0
i2p_p2i	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.13	0.00	0.12
largeObjects	0	0	0
ldOpts	0.02	0.00	0.02
list.celfiles	0.03	0.00	0.12
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0