Package: ppiStats

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes ppiStats_1.8.0.tar.gz

StartedAt: 2009-04-18 17:42:31 -0700 (Sat, 18 Apr 2009)

EndedAt: 2009-04-18 17:45:51 -0700 (Sat, 18 Apr 2009)

EllapsedTime: 200.5 seconds

RetCode: 0

Status: OK

CheckDir: ppiStats.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/ppiStats.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'ppiStats/DESCRIPTION' ... OK
* this is package 'ppiStats' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ppiStats' 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating ppiStats-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating ppiStats-manual.tex ... OK
* checking ppiStats-manual.tex using pdflatex ... OK

* Installing *source* package 'ppiStats' ...
** R
** inst
** preparing package for lazy loading
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: GOstats
Loading required package: graph
Loading required package: annotate
Loading required package: xtable
Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: org.Sc.sgd.db
Loading required package: ppiData
Loading required package: Rgraphviz
Loading required package: grid

Attaching package: 'Rgraphviz'


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

	 toFile 

Loading required package: ScISI
Loading required package: apComplex
Loading required package: RpsiXML
Loading required package: XML

Attaching package: 'XML'


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

	 addNode 

Loading required package: hypergraph

Attaching package: 'hypergraph'


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

	 head,
	 tail 


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

	 label,
	 label<- 


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

	 head,
	 tail 


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

	 head,
	 tail 

Loading required package: lattice
Loading required package: RColorBrewer
** help
 >>> Building/Updating help pages for package 'ppiStats'
     Formats: text html latex example 
  assessSymmetry                    text    html    latex   example
  bpMatrix                          text    html    latex   example
  calcInOutDegStats                 text    html    latex   example
  createSummaryTables               text    html    latex   example
  degreeEstimates                   text    html    latex   example
  estErrProbMethodOfMoments         text    html    latex   example
  estimateCCMErrorRates             text    html    latex   example
  estimatePPIErrorRates             text    html    latex   example
Note: removing empty section \examples in file 'findAdjacent.Rd'
  findAdjacent                      text    html    latex
  genBPGraph                        text    html    latex   example
Note: removing empty section \references in file 'hgParams.Rd'
Note: removing empty section \examples in file 'hgParams.Rd'
  hgParams                          text    html    latex
Note: removing empty section \references in file 'hgTests.Rd'
Note: removing empty section \examples in file 'hgTests.Rd'
  hgTests                           text    html    latex
  idProteinErrorType                text    html    latex   example
  idProteinType                     text    html    latex   example
  inOutScatterCharts                text    html    latex   example
  nullDistDoublyTestedEdges         text    html    latex   example
  separateExptBySize                text    html    latex
  twPERM                            text    html    latex   example
  viabilityCharts                   text    html    latex   example
** building package indices ...
* DONE (ppiStats)