Package: oligoClasses

Version: 1.9.14

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes oligoClasses_1.9.14.tar.gz

StartedAt: 2009-12-07 18:08:50 -0800 (Mon, 07 Dec 2009)

EndedAt: 2009-12-07 18:11:21 -0800 (Mon, 07 Dec 2009)

EllapsedTime: 150.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 2

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/oligoClasses.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-30 r50622)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.9.14'
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning in get_S4_generics_with_methods(code_env) :
  Generics g in env = <environment: package:oligoClasses> where hasMethods(g, env) errors: ‘width’
May need something like

  importFrom("IRanges", "width")

in NAMESPACE.
Warning in methods::findMethods(g, env) :
  non-generic function 'end' given to findMethods()
Warning in methods::findMethods(g, env) :
  non-generic function 'start' given to findMethods()
Warning in methods::findMethods(g, env) :
  non-generic function 'width' given to findMethods()
Undocumented code objects:
  CA CA<- CB CB<- addFeatureAnnotation.pd allele bothStrands calls
  calls<- callsConfidence callsConfidence<- chromosome chromosome<-
  cnConfidence cnConfidence<- confs confs<- copyNumber copyNumber<-
  emissionPr emissionPr<- rangedData rangedData<- segmentData
  segmentData<-
Undocumented S4 classes:
  AlleleSet CNSet SnpSuperSet
Undocumented S4 methods:
  generic 'CA' and siglist 'CNSet'
  generic 'CA<-' and siglist 'CNSet,matrix'
  generic 'CB' and siglist 'CNSet'
  generic 'CB<-' and siglist 'CNSet,matrix'
  generic 'allele' and siglist 'AlleleSet'
  generic 'annotation' and siglist 'DBPDInfo'
  generic 'bothStrands' and siglist 'AlleleSet'
  generic 'calls' and siglist 'SnpSet'
  generic 'calls<-' and siglist 'SnpSet,matrix'
  generic 'callsConfidence' and siglist 'SnpSet'
  generic 'callsConfidence<-' and siglist 'SnpSet,matrix'
  generic 'chromosome' and siglist 'SnpSet'
  generic 'chromosome<-' and siglist 'SnpSet'
  generic 'combine' and siglist 'SnpSet,SnpSet'
  generic 'confs' and siglist 'SnpSet'
  generic 'confs<-' and siglist 'SnpSet,matrix'
  generic 'db' and siglist 'AlleleSet'
  generic 'db' and siglist 'SnpSet'
  generic 'emissionPr' and siglist 'CNSet'
  generic 'emissionPr<-' and siglist 'CNSet,array'
  generic 'getA' and siglist 'AlleleSet'
  generic 'getM' and siglist 'AlleleSet'
  generic 'initialize' and siglist 'CNSet'
  generic 'position' and siglist 'SnpSet'
  generic 'rangedData' and siglist 'CNSet'
  generic 'rangedData<-' and siglist 'CNSet,RangedData'
  generic 'segmentData' and siglist 'CNSet'
  generic 'segmentData<-' and siglist 'CNSet,RangedData'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Warning in get_S4_generics_with_methods(code_env) :
  Generics g in env = <environment: package:oligoClasses> where hasMethods(g, env) errors: ‘width’
May need something like

  importFrom("IRanges", "width")

in NAMESPACE.
Warning in methods::findMethods(g, env) :
  non-generic function 'end' given to findMethods()
Warning in methods::findMethods(g, env) :
  non-generic function 'start' given to findMethods()
Warning in methods::findMethods(g, env) :
  non-generic function 'width' given to findMethods()
Warning in get_S4_generics_with_methods(code_env) :
  Generics g in env = <environment: package:oligoClasses> where hasMethods(g, env) errors: ‘width’
May need something like

  importFrom("IRanges", "width")

in NAMESPACE.
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  /Users/biocbuild/bbs-2.6-bioc/meat/oligoClasses.Rcheck/00check.log
for details

* 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)'.

** help
*** installing help indices
** building package indices ...
* DONE (oligoClasses)