Package: oligoClasses

Version: 1.14.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.14.0.tar.gz

StartedAt: 2011-10-20 15:40:24 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:42:28 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 123.4 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/oligoClasses.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.14.0'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 1.14.0
  ================================================================================
  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

* installing *source* package 'oligoClasses' ...
** R
** data
** inst
** preparing package for lazy loading
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 1.14.0
================================================================================
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)

name	user	system	elapsed
AlleleSet-class	0.26	0.00	0.26
AssayData-methods	0.63	0.00	0.63
CNSet-class	8.54	0.05	8.72
FeatureSetExtensions-class	0.33	0.01	0.35
PDInfo-methods	1.19	0.03	1.26
SnpSet-methods	0.21	0.02	0.22
SnpSuperSet-class	0.25	0.00	0.25
addFeatureAnnotation	4.01	0.05	4.19
affyPlatforms	0	0	0
batch	0.42	0.01	0.43
celfileDate	0.07	0.00	0.41
checkExists	0.01	0.00	0.01
chromosome2integer	0	0	0
data-efsExample	0	0	0
data-scqsExample	0	0	0
data-sfsExample	0.02	0.00	0.02
data-sqsExample	0	0	0
db	0	0	0
ff_matrix	0	0	0
fileConnections	0	0	0
flags	0.2	0.0	0.2
getBar	0	0	0
i2p_p2i	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.13	0.02	0.14
largeObjects	0	0	0
ldOpts	0	0	0
list.celfiles	0.17	0.00	0.25
pdPkgFromBioC	0	0	0
relocateObject	0	0	0
requireAnnotation	0	0	0
splitVec	0.00	0.01	0.02