Package: AnnotationDbi

Version: 0.0.76

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check AnnotationDbi_0.0.76.tar.gz

RetCode: 1

Time: 111.0 seconds

Status: ERROR

CheckDir: AnnotationDbi.Rcheck

Warnings: NA

* 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 '0.0.76'
* 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 checkProperty0 collabels
  count.left.mappedNames count.links count.mappedNames
  count.right.mappedNames createAnnObjs.AFFYHUEX_DB createAnnObjs.AG_DB
  createAnnObjs.GO_DB createAnnObjs.HGU95AV2_DB
  createAnnObjs.LLMAPPINGS_DB createAnnObjs.YEAST2_DB
  createAnnObjs.YEAST_DB db dbFileConnect dbFileDisconnect flatten
  foldListOfAtomicVectors foldListOfLists from.colpos from.names
  left.colname left.filter left.length left.mappedNames left.names
  left.table links mappedNames mergeToNamespaceAndExport revmap
  right.colname right.filter right.length right.mappedNames right.names
  right.table tags.colpos to.colpos toList to.names toTable
Undocumented S4 classes:
  AnnDbMap AnnDbObj AnnDbTable AtomicAnnDbMap BimapAPI0 FlatBimap
  Go3AnnDbMap GoAnnDbMap GONodeAnnDbMap IpiAnnDbMap L2Rbrick
  RevAnnDbMap RevAtomicAnnDbMap RevGo3AnnDbMap RevGoAnnDbMap
  RevGONodeAnnDbMap
Undocumented S4 methods:
  generic 'as.character' and siglist 'AtomicAnnDbMap'
  generic 'as.character' and siglist 'RevAtomicAnnDbMap'
  generic 'as.list' and siglist 'AtomicAnnDbMap'
  generic 'as.list' and siglist 'RevAtomicAnnDbMap'
  generic 'as.list' and siglist 'IpiAnnDbMap'
  generic 'as.list' and siglist 'GoAnnDbMap'
  generic 'as.list' and siglist 'RevGoAnnDbMap'
  generic 'as.list' and siglist 'RevGo3AnnDbMap'
  generic 'as.list' and siglist 'GONodeAnnDbMap'
  generic '[[' and siglist 'AnnDbMap'
  generic '$' and siglist 'AnnDbMap'
  generic 'collabels' and siglist 'FlatBimap'
  generic 'collabels' and siglist 'AnnDbMap'
  generic 'colnames' and siglist 'FlatBimap'
  generic 'colnames' and siglist 'AnnDbMap'
  generic 'count.left.mappedNames' and siglist 'BimapAPI0'
  generic 'count.left.mappedNames' and siglist 'AnnDbMap'
  generic 'count.left.mappedNames' and siglist 'Go3AnnDbMap'
  generic 'count.links' and siglist 'BimapAPI0'
  generic 'count.links' and siglist 'AnnDbMap'
  generic 'count.mappedNames' and siglist 'AnnDbMap'
  generic 'count.mappedNames' and siglist 'RevAnnDbMap'
  generic 'count.mappedNames' and siglist 'environment'
  generic 'count.right.mappedNames' and siglist 'BimapAPI0'
  generic 'count.right.mappedNames' and siglist 'AnnDbMap'
  generic 'count.right.mappedNames' and siglist 'Go3AnnDbMap'
  generic 'db' and siglist 'AnnDbObj'
  generic 'dim' and siglist 'BimapAPI0'
  generic 'eapply' and siglist 'AnnDbMap'
  generic 'exists' and siglist 'ANY,ANY,AnnDbMap'
  generic 'exists' and siglist 'ANY,AnnDbMap,missing'
  generic 'flatten' and siglist 'AnnDbMap'
  generic 'flatten' and siglist 'Go3AnnDbMap'
  generic 'from.colpos' and siglist 'BimapAPI0'
  generic 'from.names' and siglist 'BimapAPI0'
  generic 'get' and siglist 'ANY,ANY,AnnDbMap'
  generic 'get' and siglist 'ANY,AnnDbMap,missing'
  generic 'head' and siglist 'FlatBimap'
  generic 'initialize' and siglist 'FlatBimap'
  generic 'initialize' and siglist 'GONode'
  generic 'initialize' and siglist 'L2Rbrick'
  generic 'initialize' and siglist 'AnnDbPkgSeed'
  generic 'is.na' and siglist 'AnnDbMap'
  generic 'left.colname' and siglist 'BimapAPI0'
  generic 'left.filter' and siglist 'AnnDbMap'
  generic 'left.length' and siglist 'BimapAPI0'
  generic 'left.length' and siglist 'AnnDbMap'
  generic 'left.mappedNames' and siglist 'FlatBimap'
  generic 'left.mappedNames' and siglist 'AnnDbMap'
  generic 'left.mappedNames' and siglist 'Go3AnnDbMap'
  generic 'left.names' and siglist 'FlatBimap'
  generic 'left.names' and siglist 'AnnDbMap'
  generic 'left.table' and siglist 'AnnDbMap'
  generic 'length' and siglist 'AnnDbMap'
  generic 'length' and siglist 'RevAnnDbMap'
  generic 'links' and siglist 'FlatBimap'
  generic 'links' and siglist 'AnnDbMap'
  generic 'ls' and siglist 'AnnDbMap'
  generic 'mappedNames' and siglist 'AnnDbMap'
  generic 'mappedNames' and siglist 'RevAnnDbMap'
  generic 'mappedNames' and siglist 'environment'
  generic 'mget' and siglist 'ANY,AnnDbMap'
  generic 'mget' and siglist 'ANY,RevAnnDbMap'
  generic 'names' and siglist 'AnnDbMap'
  generic 'names' and siglist 'RevAnnDbMap'
  generic 'ncol' and siglist 'BimapAPI0'
  generic 'nrow' and siglist 'FlatBimap'
  generic 'nrow' and siglist 'AnnDbTable'
  generic 'nrow' and siglist 'AnnDbMap'
  generic 'nrow' and siglist 'Go3AnnDbMap'
  generic 'revmap' and siglist 'AtomicAnnDbMap'
  generic 'revmap' and siglist 'RevAtomicAnnDbMap'
  generic 'revmap' and siglist 'GoAnnDbMap'
  generic 'revmap' and siglist 'RevGoAnnDbMap'
  generic 'revmap' and siglist 'Go3AnnDbMap'
  generic 'revmap' and siglist 'RevGo3AnnDbMap'
  generic 'revmap' and siglist 'environment'
  generic 'right.colname' and siglist 'BimapAPI0'
  generic 'right.filter' and siglist 'AnnDbMap'
  generic 'right.length' and siglist 'BimapAPI0'
  generic 'right.length' and siglist 'AnnDbMap'
  generic 'right.length' and siglist 'Go3AnnDbMap'
  generic 'right.mappedNames' and siglist 'FlatBimap'
  generic 'right.mappedNames' and siglist 'AnnDbMap'
  generic 'right.mappedNames' and siglist 'Go3AnnDbMap'
  generic 'right.names' and siglist 'FlatBimap'
  generic 'right.names' and siglist 'AnnDbMap'
  generic 'right.names' and siglist 'Go3AnnDbMap'
  generic 'right.table' and siglist 'AnnDbMap'
  generic 'right.table' and siglist 'Go3AnnDbMap'
  generic 'sample' and siglist 'AnnDbMap'
  generic 'show' and siglist 'FlatBimap'
  generic 'show' and siglist 'L2Rbrick'
  generic 'show' and siglist 'AnnDbTable'
  generic 'show' and siglist 'AnnDbMap'
  generic 'tags.colpos' and siglist 'BimapAPI0'
  generic 'tail' and siglist 'FlatBimap'
  generic 'to.colpos' and siglist 'BimapAPI0'
  generic 'toList' and siglist 'AnnDbMap'
  generic 'toList' and siglist 'RevAnnDbMap'
  generic 'to.names' and siglist 'BimapAPI0'
  generic 'toTable' and siglist 'AnnDbMap'
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 ... ERROR
Running examples in 'AnnotationDbi-Ex.R' failed.
The error most likely occurred in:

> ### * GONode-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: GONode-class
> ### Title: Class "GONode"
> ### Aliases: class:GONode GONode-class GONode GOID Term Ontology Definition
> ###   Synonym Secondary GOID,GONode-method Term,GONode-method
> ###   Ontology,GONode-method Definition,GONode-method Synonym,GONode-method
> ###   Secondary,GONode-method show,GONode-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>   gonode <- new("GONode", GOID="GO:1234567", Term="Test", Ontology="MF")
Error in initialize(value, ...) : arguments GOID, Term, Ontology, Definition are mandatory
Execution halted

* 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 "ncol" in "AnnotationDbi"
Creating a new generic function for "colnames" in "AnnotationDbi"
Creating a new generic function for "nrow" in "AnnotationDbi"
Creating a new generic function for "head" in "AnnotationDbi"
Creating a new generic function for "tail" in "AnnotationDbi"
Creating a new generic function for "toString" in "AnnotationDbi"
Creating a new generic function for "rev" 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"
Creating a new generic function for "sample" in "AnnotationDbi"
** help
 >>> Building/Updating help pages for package 'AnnotationDbi'
     Formats: text html latex example 
  AnnDbPkgSeed-class                text    html    latex   example
  GONode-class                      text    html    latex   example
  makeAnnDbPkg                      text    html    latex   example
** building package indices ...
* DONE (AnnotationDbi)