Package: Rintact

Version: 0.3.29

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check Rintact_0.3.29.tar.gz

RetCode: 0

Time: 160.3 seconds

Status: WARNINGS

CheckDir: Rintact.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/Rintact.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'Rintact/DESCRIPTION' ... OK
* this is package 'Rintact' version '0.3.29'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rintact' 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 ... NOTE
eListHandler : startElement: no visible binding for '<<-' assignment to
  'curEL'
eListHandler : startElement: no visible binding for global variable
  'curEL'
eListHandler : text: no visible binding for global variable 'curEL'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  bait complexes interactions interactors prey
Undocumented S4 methods:
  generic 'bait' and siglist 'intactInteraction'
  generic 'complexes' and siglist 'complexEntry'
  generic 'interactions' and siglist 'interactionEntry'
  generic 'interactors' and siglist 'interactionEntry'
  generic 'interactors' and siglist 'complexEntry'
  generic 'prey' and siglist 'intactInteraction'
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 Rintact-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Rintact-manual.tex ... OK
* checking Rintact-manual.tex ... OK

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

* Installing *source* package 'Rintact' ...
** R
** inst
** preparing package for lazy loading
Loading required package: XML
Loading required package: graph
Loading required package: ppiStats
Loading required package: GO
Loading required package: GOstats
Loading required package: GO.db
Loading required package: AnnotationDbi
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

Attaching package: 'GO.db'


	The following object(s) are masked from package:GO :

	 GOBPANCESTOR,
	 GOBPCHILDREN,
	 GOBPOFFSPRING,
	 GOBPPARENTS,
	 GOCCANCESTOR,
	 GOCCCHILDREN,
	 GOCCOFFSPRING,
	 GOCCPARENTS,
	 GOMAPCOUNTS,
	 GOMFANCESTOR,
	 GOMFCHILDREN,
	 GOMFOFFSPRING,
	 GOMFPARENTS,
	 GOOBSOLETE,
	 GOSYNONYM,
	 GOTERM 

Loading required package: annotate
Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: YEAST
Loading required package: ppiData
Loading required package: Rgraphviz

Attaching package: 'Rgraphviz'


	The following object(s) are masked from package:annotate :

	 toFile 

Loading required package: hypergraph
** help
 >>> Building/Updating help pages for package 'Rintact'
     Formats: text html latex example 
  complexEntry                      text    html    latex
  eListHandler                      text    html    latex   example
  intactComplex                     text    html    latex
  intactGraph                       text    html    latex
  intactHyperGraph                  text    html    latex
  intactInteraction                 text    html    latex
  intactXML2Graph                   text    html    latex   example
  interactionEntry                  text    html    latex
  list2Matrix                       text    html    latex   example
  psi25interaction                  text    html    latex   example
  translateIntactID                 text    html    latex   example
** building package indices ...
* DONE (Rintact)