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Package 281/419HostnameOS / ArchBUILDCHECKBUILD BIN
oligoClasses 1.12.2
Benilton Carvalho and Robert Scharpf
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/oligoClasses
Last Changed Rev: 51940 / Revision: 54588
Last Changed Date: 2011-01-16 12:00:12 -0800 (Sun, 16 Jan 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 

Summary

Package: oligoClasses
Version: 1.12.2
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.12.2.tar.gz
StartedAt: 2011-04-07 07:57:58 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:59:51 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 113.6 seconds
RetCode: 0
Status:  OK 
CheckDir: oligoClasses.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/oligoClasses.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.12.2’
* 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

oligoClasses.Rcheck/00install.out:

* 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)

oligoClasses.Rcheck/oligoClasses-Ex.timings:

nameusersystemelapsed
AlleleSet-class0.2960.0000.299
AssayData-methods0.7280.0120.738
CNSet-class9.4680.1209.648
FeatureSetExtensions-class0.3560.0120.366
PDInfo-methods0.5280.0320.561
SnpSet-methods0.3880.0120.431
SnpSuperSet-class0.1000.0000.098
addFeatureAnnotation4.0080.0524.154
affyPlatforms000
batch0.4520.0280.482
celfileDate0.0440.0000.098
checkExists0.0040.0040.006
chromosome2integer000
data-efsExample0.0040.0000.003
data-scqsExample0.0000.0000.002
data-sfsExample0.0000.0000.001
data-sqsExample0.0000.0000.002
db000
ff_matrix0.0000.0000.001
flags0.1840.0000.184
getBar000
i2p_p2i000
is.ffmatrix0.0000.0000.001
isPackageLoaded000
kind0.1120.0120.122
largeObjects000
ldOpts0.0000.0000.002
list.celfiles0.0280.0040.047
pdPkgFromBioC000
requireAnnotation000
splitVec0.0040.0000.001