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Package 260/389HostnameOS / ArchBUILDCHECKBUILD BIN
oligoClasses 1.10.0
Benilton Carvalho and Robert Scharpf
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/oligoClasses
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / 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 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: oligoClasses
Version: 1.10.0
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.10.0.tar.gz
StartedAt: 2010-10-04 18:52:01 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 18:53:49 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 108.0 seconds
RetCode: 0
Status:  OK 
CheckDir: oligoClasses.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/oligoClasses.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.10.0'
* 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'
initializeBigMatrix: no visible binding for global variable 'ffdf'
initializeBigVector: no visible global function definition for 'ff'
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'
getA,AlleleSet: no visible global function definition for 'ff'
getM,AlleleSet: no visible global function definition for 'ff'
* checking Rd files ... OK
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

oligoClasses.Rcheck/00install.out:

* install options are ' --no-html'

* 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)'.

in method for 'annotatedDataFrameFrom' with signature '"ff_matrix"': no definition for class "ff_matrix"
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 1.10.0
================================================================================
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-class0.0000.0000.002
CNSet-class000
FeatureSetExtensions-class0.5200.0000.519
PDInfo-methods0.6600.0280.688
SnpSet-methods0.0680.0000.069
SnpSuperSet-class0.0040.0000.001
addFeatureAnnotation17.709 0.28818.317
affyPlatforms000
celfileDate0.0400.0080.146
chromosome2integer000
data-efsExample0.0000.0000.003
data-scqsExample0.0000.0000.002
data-sfsExample0.0000.0040.002
data-sqsExample0.0000.0000.002
db000
getBar000
is.ffmatrix0.0000.0000.001
isPackageLoaded0.0000.0000.001
kind0.3400.0200.363
largeObjects0.0040.0000.001
ldOpts0.0000.0000.002
list.celfiles0.0280.0080.090
pdPkgFromBioC0.0000.0000.001
requireAnnotation000
splitVec0.0000.0040.002