Package: AnnotationDbi

Version: 0.0.8

Command: /loc/biocbuild/2.0d/R/bin/R CMD check AnnotationDbi_0.0.8.tar.gz

RetCode: 0

Time: 53.8 seconds

Status: WARNINGS

CheckDir: AnnotationDbi.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/2.0d/Rpacks/AnnotationDbi.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'AnnotationDbi/DESCRIPTION' ... OK
* this is package 'AnnotationDbi' version '0.0.8'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  pkg1 pkg2
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... 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 S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  allFeatureSetIds allMMIds allPMAllele allPMIds allPMStrand
  compareAnnotation comparePerf countBy generateAnnotTableObj
  generateQC generateTableObjects generateTwoWayMappings getCol
  noMissing pmFeatures pmIdsByAllele1 pmIdsByAllele2 queryTable
  subByRow toggleDebug userTable
Undocumented S4 classes:
  AnnotDbEnv AnnotDbTable AnnotDbTableTwoWayMap AnnotGOTermsTable
  AnnotMultiColTable AnnotThreeColTable AnnotTwoColTable functionORNULL
  PDInfo SNPPDInfo SQLiteAnnDataPkgSeed
Undocumented S4 methods:
  generic 'as.list' and siglist 'AnnotDbTableTwoWayMap'
  generic 'as.list' and siglist 'AnnotMultiColTable'
  generic 'as.list' and siglist 'AnnotMultiColTwoKeyTable'
  generic 'as.list' and siglist 'AnnotGOTermsTable'
  generic 'as.list' and siglist 'AnnotThreeColTable'
  generic '[' and siglist 'AnnotDbTable,vector,missing,missing'
  generic '[[' and siglist 'AnnotDbTable,vector,missing'
  generic '$' and siglist 'AnnotDbEnv,character'
  generic '$' and siglist 'AnnotDbTable,character'
  generic 'contents' and siglist 'AnnotDbTable'
  generic 'countBy' and siglist 'AnnotDbTableTwoWayMap,ANY,missing'
  generic 'countBy' and siglist 'AnnotMultiColTable,ANY,missing'
  generic 'countBy' and siglist 'AnnotDbTable,ANY,character'
  generic 'dbGetQuery' and siglist 'AnnotDbTable,character'
  generic 'dim' and siglist 'AnnotDbTable'
  generic 'eapply' and siglist 'AnnotDbTable,function'
  generic 'get' and siglist
    'vector,missing,AnnotDbTable,missing,missing'
  generic 'get' and siglist
    'vector,AnnotDbTable,missing,missing,missing'
  generic 'getCol' and siglist 'AnnotDbTable,character'
  generic 'getCol' and siglist 'AnnotDbTableTwoWayMap,character'
  generic 'initialize' and siglist 'AnnotDbTable'
  generic 'initialize' and siglist 'AnnotDbTableTwoWayMap'
  generic 'initialize' and siglist 'AnnotMultiColTable'
  generic 'initialize' and siglist 'AnnotMultiColTwoKeyTable'
  generic 'initialize' and siglist 'AnnotThreeColTable'
  generic 'is.environment' and siglist 'AnnotDbEnv'
  generic 'length' and siglist 'AnnotMultiColTable'
  generic 'length' and siglist 'AnnotDbTableTwoWayMap'
  generic 'ls' and siglist
    'AnnotDbTableTwoWayMap,missing,missing,missing,missing'
  generic 'ls' and siglist
    'AnnotMultiColTable,missing,missing,missing,missing'
  generic 'makeDataPackage' and siglist 'SQLiteAnnDataPkgSeed'
  generic 'mget' and siglist
    'vector,AnnotDbTableTwoWayMap,missing,missing,missing'
  generic 'mget' and siglist
    'vector,AnnotMultiColTwoKeyTable,missing,missing,missing'
  generic 'mget' and siglist
    'vector,AnnotMultiColTable,missing,missing,missing'
  generic 'mget' and siglist
    'vector,AnnotGOTermsTable,missing,missing,missing'
  generic 'mget' and siglist
    'vector,AnnotThreeColTable,missing,missing,missing'
  generic 'mget' and siglist
    'vector,AnnotDbTable,missing,logical,missing'
  generic 'mget' and siglist 'vector,AnnotDbTable,missing,list,missing'
  generic 'names' and siglist 'AnnotDbTable'
  generic 'ncol' and siglist 'AnnotDbTable'
  generic 'noMissing' and siglist 'AnnotMultiColTwoKeyTable,character'
  generic 'noMissing' and siglist 'AnnotMultiColTable,character'
  generic 'noMissing' and siglist 'AnnotGOTermsTable,character'
  generic 'noMissing' and siglist 'AnnotThreeColTable,character'
  generic 'noMissing' and siglist 'AnnotDbTableTwoWayMap,character'
  generic 'noMissing' and siglist 'AnnotDbTableTwoWayMap,missing'
  generic 'nrow' and siglist 'AnnotDbTable'
  generic 'queryTable' and siglist 'AnnotDbTable'
  generic 'show' and siglist 'AnnotDbTable'
  generic 'subByRow' and siglist
    'AnnotMultiColTwoKeyTable,character,list'
  generic 'subByRow' and siglist 'AnnotMultiColTable,character,list'
  generic 'subByRow' and siglist 'AnnotGOTermsTable,character,list'
  generic 'subByRow' and siglist 'AnnotThreeColTable,character,list'
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 DVI version of manual ... OK

WARNING: There were 2 warnings, see
  /extra/loc/biocbuild/2.0d/Rpacks/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()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: RSQLite
Loading required package: DBI
Creating a new generic function for "as.list" in "AnnotationDbi"
Creating a new generic function for "eapply" in "AnnotationDbi"
Creating a new generic function for "mget" in "AnnotationDbi"
Creating a new generic function for "get" in "AnnotationDbi"
Creating a new generic function for "names" in "AnnotationDbi"
Creating a new generic function for "nrow" in "AnnotationDbi"
Creating a new generic function for "ls" in "AnnotationDbi"
No man pages found in package 'AnnotationDbi'
** building package indices ...
* DONE (AnnotationDbi)