Package: oligoClasses

Version: 1.13.9

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.13.9.tar.gz

StartedAt: 2011-02-24 20:35:34 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:37:51 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 137.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/oligoClasses.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.13.9’
* 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
Warning in methods::findMethods(g, where = env) :
  non-generic function 'relocateObject' given to findMethods()
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’
ocProbesets: no visible global function definition for ‘clusterCall’
ocSamples: no visible global function definition for ‘clusterCall’
relocateObject : f2: no visible global function definition for
  ‘physical<-’
relocateObject: no visible global function definition for ‘physical<-’
relocateObject : relocate.fxn: no visible binding for global variable
  ‘nmm’
relocateObject : relocate.fxn: no visible global function definition
  for ‘filename<-’
relocateObject : relocate.fxn: no visible global function definition
  for ‘physical<-’
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,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: batch.Rd:44-46: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'allele' and siglist 'SnpFeatureSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 1.13.9
  ================================================================================
  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

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.8-bioc/meat/oligoClasses.Rcheck/00check.log’
for details

* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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 1.13.9
================================================================================
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	0.334	0.004	0.339
AssayData-methods	0.868	0.037	0.908
CNSet-class	11.017	0.227	11.318
FeatureSetExtensions-class	0.893	0.026	0.925
PDInfo-methods	0.646	0.048	0.695
SnpSet-methods	0.399	0.019	0.504
SnpSuperSet-class	0.315	0.001	0.317
addFeatureAnnotation	5.250	0.135	5.512
affyPlatforms	0.001	0.000	0.001
batch	0.966	0.031	1.013
celfileDate	0.046	0.006	0.157
checkExists	0.011	0.002	0.012
chromosome2integer	0.001	0.000	0.001
data-efsExample	0.004	0.001	0.005
data-scqsExample	0.003	0.001	0.004
data-sfsExample	0.003	0.001	0.004
data-sqsExample	0.003	0.000	0.004
db	0.001	0.000	0.000
ff_matrix	0.001	0.000	0.001
flags	0.412	0.022	0.440
getBar	0.001	0.000	0.001
i2p_p2i	0.000	0.000	0.001
is.ffmatrix	0.001	0.000	0.001
isPackageLoaded	0.001	0.000	0.001
kind	0.189	0.014	0.213
largeObjects	0.001	0.000	0.001
ldOpts	0.002	0.000	0.003
list.celfiles	0.043	0.005	0.217
pdPkgFromBioC	0.000	0.000	0.001
relocateObject	0.000	0.000	0.001
requireAnnotation	0.000	0.000	0.001
splitVec	0.001	0.001	0.003