Package: oligoClasses

Version: 1.12.2

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.12.2.tar.gz

StartedAt: 2011-03-31 07:00:34 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:03:17 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 163.0 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/oligoClasses.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* 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 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’
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	0.324	0.005	0.335
AssayData-methods	0.853	0.041	0.915
CNSet-class	10.828	0.235	11.197
FeatureSetExtensions-class	0.975	0.030	1.012
PDInfo-methods	0.638	0.049	0.695
SnpSet-methods	0.378	0.020	0.474
SnpSuperSet-class	0.295	0.002	0.302
addFeatureAnnotation	5.246	0.141	5.556
affyPlatforms	0.001	0.000	0.002
batch	0.933	0.031	0.969
celfileDate	0.047	0.006	0.171
checkExists	0.011	0.002	0.082
chromosome2integer	0.001	0.001	0.000
data-efsExample	0.004	0.000	0.004
data-scqsExample	0.003	0.000	0.004
data-sfsExample	0.003	0.000	0.004
data-sqsExample	0.003	0.000	0.003
db	0	0	0
ff_matrix	0.001	0.000	0.001
flags	0.403	0.022	0.428
getBar	0.000	0.000	0.001
i2p_p2i	0.000	0.001	0.001
is.ffmatrix	0.001	0.000	0.002
isPackageLoaded	0.000	0.001	0.001
kind	0.176	0.012	0.190
largeObjects	0.001	0.000	0.001
ldOpts	0.003	0.000	0.002
list.celfiles	0.043	0.005	0.069
pdPkgFromBioC	0	0	0
requireAnnotation	0.000	0.001	0.000
splitVec	0.002	0.001	0.003