Package: oligoClasses

Version: 1.15.9

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.15.9.tar.gz

StartedAt: 2011-07-07 01:38:02 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:40:18 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 136.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/oligoClasses.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.15.9’
* 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 installed package size ... 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’
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 ... WARNING
Undocumented code objects:
  ‘isFF’
Undocumented S4 methods:
  generic 'close' and siglist 'array'
  generic 'open' and siglist 'array'
  generic 'show' and siglist 'CNSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 1.15.9
  ================================================================================
  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 data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-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 generic function for "close" from package "base" in package “oligoClasses”
Creating a generic function for "open" from package "base" in package “oligoClasses”
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
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	0.332	0.008	0.342
AssayData-methods	0.852	0.016	0.872
CNSet-class	11.113	0.224	11.781
FeatureSetExtensions-class	0.404	0.000	0.405
PDInfo-methods	1.296	0.008	1.377
SnpSet-methods	0.296	0.004	0.306
SnpSuperSet-class	0.280	0.000	0.279
addFeatureAnnotation	4.268	0.100	4.467
affyPlatforms	0	0	0
batch	0.412	0.016	0.434
celfileDate	0.020	0.000	0.022
checkExists	0.004	0.000	0.006
chromosome2integer	0	0	0
data-efsExample	0.008	0.000	0.003
data-scqsExample	0.000	0.000	0.002
data-sfsExample	0.004	0.000	0.002
data-sqsExample	0.000	0.000	0.002
db	0.000	0.000	0.001
ff_matrix	0.000	0.000	0.001
fileConnections	0.000	0.000	0.001
flags	0.176	0.000	0.176
getBar	0.000	0.000	0.001
i2p_p2i	0.000	0.000	0.001
is.ffmatrix	0.000	0.000	0.001
isPackageLoaded	0.000	0.000	0.001
kind	0.096	0.008	0.102
largeObjects	0.004	0.000	0.001
ldOpts	0.000	0.000	0.001
list.celfiles	0.02	0.00	0.04
pdPkgFromBioC	0	0	0
relocateObject	0	0	0
requireAnnotation	0	0	0
splitVec	0.004	0.000	0.002