Package: GSEABase

Version: 0.2.27

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check GSEABase_0.2.27.tar.gz

RetCode: 0

Time: 220.5 seconds

Status: WARNINGS

CheckDir: GSEABase.Rcheck

Warnings: 3

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/GSEABase.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '0.2.27'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GSEABase' 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:
  evidenceCode<- goIds<- keggIds keggIds<-
Undocumented S4 methods:
  generic '[[<-' and siglist 'GeneSetCollection,ANY,ANY,GeneSet'
  generic 'evidenceCode<-' and siglist 'GOCollection,character'
  generic 'goIds<-' and siglist 'GOCollection,character'
  generic 'keggIds<-' and siglist 'KEGGCollection,character'
  generic 'keggIds' and siglist 'KEGGCollection'
  generic 'setdiff' and siglist 'GeneSetCollection,GeneSetCollection'
  generic 'show' and siglist 'KEGGCollection'
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
Codoc mismatches from documentation object 'CollectionType':
KEGGCollection
  Code: function(keggIds = as.character(NA))
  Docs: function(...)
  Argument names in code not in docs:
    keggIds
  Argument names in docs not in code:
    ...
  Mismatches in argument names:
    Position: 1 Code: keggIds Docs: ...

Codoc mismatches from documentation object 'xal':
getBroadSets
  Code: function(uri, ...)
  Docs: function(file, ...)
  Argument names in code not in docs:
    uri
  Argument names in docs not in code:
    file
  Mismatches in argument names:
    Position: 1 Code: uri Docs: file
asBroadUri
  Code: function(name, base =
                 "http://www.broad.mit.edu/gsea/msigdb/cards")
  Docs: function(name, base =
                 "http://www.broad.mit.edu/gsea/msigdb/card")
  Mismatches in argument default values:
    Name: base Code: http://www.broad.mit.edu/gsea/msigdb/cards Docs: http://www.broad.mit.edu/gsea/msigdb/card

* checking Rd \usage sections ... OK
* creating GSEABase-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
<?xml version="1.0"?>
<GENESET STANDARD_NAME="chr5q23" SYSTEMATIC_NAME="c1:101" ORGANISM="Human" EXTERNAL_DETAILS_URL="file://extra/loc/biocbuild/bbs-2.1-bioc/meat/GSEABase.Rcheck/GSEABase/extdata/Broad.xml,http://www.broad.mit.edu/gsea/msigdb/cards/chr5q23.xml,http://genome.ucsc.edu/cgi-bin/hgTracks?position=5q23" CATEGORY_CODE="c1" CONTRIBUTOR="Broad Institute" DESCRIPTION_FULL="Genes in cytogenetic band chr5q23" DESCRIPTION_BRIEF="Genes in cytogenetic band chr5q23" MEMBERS_SYMBOLIZED="ZNF474,CCDC100,ANKRD43,NRG2,LOC391828,IL4,PACAP,SLC12A2,LOC644659,DTWD2,PRRC1,EGR1,LOC389322,FNIP1,MGC32805,SRFBP1,CSNK1G3,LOC644854,PGGT1B,LOC728682,FLJ33630,LOC644754,CAMLG,CSS3,LOX,UBE2B,FTMT,LOC728460,GDF9,LOC644146,LOC728711,LOC728342,CDO1,LOC402229,ADRA1B,MRPS5P3,LMNB1,NME5,LOC644100,LOC391827,RNF14,LOC391825,NEUROG1,LOC474341,FBN2,LOC133629,PRR16,LOC728612,ITGA2,FABP6,IRF1,FLJ27505,SLC27A6,PPIC,LOC391824,CSF2,LOC348958,LOC644557,ADAMTS2,SNX2,ARGFXP1,RPS17P2,GPX3,ZNF608,GRAMD3,IL5,CTXN3,HBEGF,IL3,LOC401206,RAD50,SNX24,ACTBP4,LOC153277,LOC340069,FLJ44606,LOC133609,PPP2CA,COMMD10,RNUXA,TNFAIP8,MARCH3,FLJ90650,PTMAP2,SEMA6A,LOC728586"/>
--- running texi2dvi on vignettes
* creating GSEABase-manual.tex ... OK
* checking GSEABase-manual.tex ... OK

WARNING: There were 3 warnings, see
  /extra/loc/biocbuild/bbs-2.1-bioc/meat/GSEABase.Rcheck/00check.log
for details

* Installing *source* package 'GSEABase' ...
** 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: XML
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
** help
 >>> Building/Updating help pages for package 'GSEABase'
     Formats: text html latex example 
  CollectionType-class              text    html    latex   example
  CollectionType-constructors       text    html    latex   example
  GSEABase-package                  text    html    latex   example
  GeneColorSet-class                text    html    latex   example
  GeneColorSet-methods              text    html    latex
  GeneIdentifierType-class          text    html    latex   example
  GeneIdentifierType-constructors   text    html    latex   example
  GeneSet-class                     text    html    latex   example
  GeneSet-methods                   text    html    latex   example
  GeneSetCollection-class           text    html    latex   example
  GeneSetCollection-methods         text    html    latex   example
  getBroadSets                      text    html    latex   example
  incidence-methods                 text    html    latex   example
  mapIdentifiers-methods            text    html    latex
** building package indices ...
* DONE (GSEABase)