Package: AnnotationDbi

Version: 0.0.64

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check AnnotationDbi_0.0.64.tar.gz

RetCode: 0

Time: 153.4 seconds

Status: WARNINGS

CheckDir: AnnotationDbi.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/AnnotationDbi.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-04-17 r41210)
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '0.0.64'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'AnnotationDbi' 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  addToNamespaceAndExport checkMAPCOUNTS compareAnnotation comparePerf
  count.mapped.left.names count.mapped.names count.mapped.right.names
  createAnnObjs.AFFYHUEX_DB createAnnObjs.AG_DB
  createAnnObjs.HGU95AV2_DB createAnnObjs.LLMAPPINGS_DB
  createAnnObjs.YEAST2_DB createAnnObjs.YEAST_DB db dbFileConnect
  dbFileDisconnect left.length left.names mapped.left.names
  mapped.names mapped.right.names mergeToNamespaceAndExport revmap
  right.length right.names toggleDebug toList toTable
Undocumented S4 classes:
  AnnMap AnnObj AnnTable AtomicAnnMap GOAnnMap IPIAnnMap ReverseAnnMap
  ReverseAtomicAnnMap ReverseGOAnnMap
Undocumented S4 methods:
  generic 'as.character' and siglist 'AtomicAnnMap'
  generic 'as.character' and siglist 'ReverseAtomicAnnMap'
  generic 'as.data.frame' and siglist 'AnnObj'
  generic 'as.list' and siglist 'AtomicAnnMap'
  generic 'as.list' and siglist 'ReverseAtomicAnnMap'
  generic 'as.list' and siglist 'IPIAnnMap'
  generic 'as.list' and siglist 'GOAnnMap'
  generic 'as.list' and siglist 'ReverseGOAnnMap'
  generic '[[' and siglist 'AnnMap'
  generic '$' and siglist 'AnnMap'
  generic 'count.mapped.left.names' and siglist 'AnnMap'
  generic 'count.mapped.left.names' and siglist 'GOAnnMap'
  generic 'count.mapped.names' and siglist 'AnnMap'
  generic 'count.mapped.names' and siglist 'ReverseAnnMap'
  generic 'count.mapped.right.names' and siglist 'AnnMap'
  generic 'count.mapped.right.names' and siglist 'GOAnnMap'
  generic 'db' and siglist 'AnnObj'
  generic 'eapply' and siglist 'AnnMap'
  generic 'exists' and siglist 'ANY,ANY,AnnMap'
  generic 'exists' and siglist 'ANY,AnnMap,missing'
  generic 'get' and siglist 'ANY,ANY,AnnMap'
  generic 'get' and siglist 'ANY,AnnMap,missing'
  generic 'initialize' and siglist 'AnnDbPkgSeed'
  generic 'is.na' and siglist 'AnnMap'
  generic 'left.length' and siglist 'AnnObj'
  generic 'left.names' and siglist 'AnnObj'
  generic 'length' and siglist 'AnnObj'
  generic 'length' and siglist 'ReverseAnnMap'
  generic 'ls' and siglist 'AnnMap'
  generic 'mapped.left.names' and siglist 'AnnMap'
  generic 'mapped.left.names' and siglist 'GOAnnMap'
  generic 'mapped.names' and siglist 'AnnMap'
  generic 'mapped.names' and siglist 'ReverseAnnMap'
  generic 'mapped.right.names' and siglist 'AnnMap'
  generic 'mapped.right.names' and siglist 'GOAnnMap'
  generic 'mget' and siglist 'ANY,AnnMap'
  generic 'mget' and siglist 'ANY,ReverseAnnMap'
  generic 'names' and siglist 'AnnObj'
  generic 'names' and siglist 'ReverseAnnMap'
  generic 'nrow' and siglist 'AnnTable'
  generic 'nrow' and siglist 'AnnMap'
  generic 'nrow' and siglist 'GOAnnMap'
  generic 'revmap' and siglist 'AtomicAnnMap'
  generic 'revmap' and siglist 'ReverseAtomicAnnMap'
  generic 'revmap' and siglist 'GOAnnMap'
  generic 'revmap' and siglist 'ReverseGOAnnMap'
  generic 'revmap' and siglist 'environment'
  generic 'right.length' and siglist 'AnnMap'
  generic 'right.length' and siglist 'GOAnnMap'
  generic 'right.names' and siglist 'AnnMap'
  generic 'right.names' and siglist 'GOAnnMap'
  generic 'show' and siglist 'AnnTable'
  generic 'show' and siglist 'AnnMap'
  generic 'toList' and siglist 'AnnMap'
  generic 'toList' and siglist 'ReverseAnnMap'
  generic 'toTable' and siglist 'AnnTable'
  generic 'toTable' and siglist 'AnnMap'
  generic 'toTable' and siglist 'GOAnnMap'
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 ... OK
* checking Rd \usage sections ... OK
* creating AnnotationDbi-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating AnnotationDbi-manual.tex ... OK
* checking AnnotationDbi-manual.tex ... OK

WARNING: There was 1 warning, see
  /extra/loc/biocbuild/bbs-2.1-bioc/meat/AnnotationDbi.Rcheck/00check.log
for details

* Installing *source* package 'AnnotationDbi' ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: RSQLite
Creating a new generic function for "as.data.frame" in "AnnotationDbi"
Creating a new generic function for "nrow" in "AnnotationDbi"
Creating a new generic function for "ls" in "AnnotationDbi"
Creating a new generic function for "as.list" in "AnnotationDbi"
Creating a new generic function for "mget" in "AnnotationDbi"
Creating a new generic function for "eapply" in "AnnotationDbi"
Creating a new generic function for "get" in "AnnotationDbi"
Creating a new generic function for "exists" in "AnnotationDbi"
** help
 >>> Building/Updating help pages for package 'AnnotationDbi'
     Formats: text html latex example 
  AnnDbPkgSeed-class                text    html    latex   example
  makeAnnDbPkg                      text    html    latex   example
** building package indices ...
* DONE (AnnotationDbi)