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Package 313/462HostnameOS / ArchBUILDCHECKBUILD BIN
oligoClasses 1.15.0
Benilton Carvalho and Robert Scharpf
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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: 1.15.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings oligoClasses_1.15.0.tar.gz
StartedAt: 2011-05-09 14:46:32 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:48:42 -0700 (Mon, 09 May 2011)
EllapsedTime: 129.9 seconds
RetCode: 0
Status:  OK  
CheckDir: oligoClasses.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/oligoClasses.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.15.0'
* 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 installed package size ... 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'
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'
* 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  ================================================================================
  Welcome to oligoClasses version 1.15.0
  ================================================================================
  Large dataset support for 'oligo/crlmm': Disabled
       - Load 'ff'
  ================================================================================
  Parallel computing support for 'oligo/crlmm': Disabled
       - Load 'ff'
       - Load 'snow'
       - Use options(cluster=makeCluster(...))
  ================================================================================
* checking data for ASCII and uncompressed saves ... OK
* 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
  '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 1.15.0
================================================================================
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-class0.250.010.27
AssayData-methods0.630.020.64
CNSet-class10.22 0.0310.42
FeatureSetExtensions-class0.690.020.70
PDInfo-methods0.620.070.71
SnpSet-methods0.060.040.09
SnpSuperSet-class0.240.000.24
addFeatureAnnotation4.370.034.51
affyPlatforms0.020.000.02
batch0.750.010.79
celfileDate0.040.000.27
checkExists000
chromosome2integer000
data-efsExample000
data-scqsExample000
data-sfsExample000
data-sqsExample000
db000
ff_matrix000
fileConnections000
flags0.310.000.31
getBar000
i2p_p2i000
is.ffmatrix000
isPackageLoaded000
kind0.110.020.13
largeObjects000
ldOpts000
list.celfiles0.010.010.08
pdPkgFromBioC000
relocateObject000
requireAnnotation000
splitVec000