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Package 243/294HostnameOS / ArchBUILDCHECKBUILD BIN
RpsiXML 1.0.0
Jitao David Zhang
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/RpsiXML
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ OK ] OK 
Package: RpsiXML
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes RpsiXML_1.0.0.tar.gz
StartedAt: 2009-04-18 18:16:38 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:19:18 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 159.8 seconds
RetCode: 0
Status: OK
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/RpsiXML.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'RpsiXML/DESCRIPTION' ... OK
* this is package 'RpsiXML' version '1.0.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RpsiXML' 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
Warning in methods::findMethods(g, where = env) :
  non-generic function 'confidenceValue' given to findMethods()
* 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 RpsiXML-Ex.R ... OK
* checking examples ... OK
* checking tests ...
  Running 'psimi25Source_test.R'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating RpsiXML-manual.tex ... OK
* checking RpsiXML-manual.tex using pdflatex ... OK

RpsiXML.Rcheck/00install.out:

* Installing *source* package 'RpsiXML' ...
** R
** inst
** preparing package for lazy loading
Loading required package: annotate
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: AnnotationDbi
Loading required package: xtable
Loading required package: XML
Loading required package: graph

Attaching package: 'graph'


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

	 addNode 

Loading required package: hypergraph

Attaching package: 'hypergraph'


	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: RBGL
** help
 >>> Building/Updating help pages for package 'RpsiXML'
     Formats: text html latex example 
  BIOGRID.PSIMI25                   text    html    latex
  availableXrefs-methods            text    html    latex
  availableXrefs                    text    html    latex   example
  bait                              text    html    latex   example
  complexName                       text    html    latex   example
  complexes                         text    html    latex   example
  eListHandler                      text    html    latex   example
  getAbstractByPMID                 text    html    latex   example
  interactionType                   text    html    latex   example
  interactions                      text    html    latex   example
  interactorInfo-methods            text    html    latex
  interactorInfo                    text    html    latex   example
  interactors-methods               text    html    latex
  interactors                       text    html    latex   example
  list2Matrix                       text    html    latex
  null2na                           text    html    latex   example
  organismName                      text    html    latex   example
  parseComplex                      text    html    latex
  parsePsimi25Interaction           text    html    latex   example
  psimi25Complex-class              text    html    latex   example
  psimi25ComplexEntry-class         text    html    latex   example
  psimi25Experiment-class           text    html    latex   example
  psimi25Graph-class                text    html    latex   example
  psimi25Hypergraph-class           text    html    latex   example
  psimi25Interaction-class          text    html    latex   example
  psimi25InteractionEntry-class     text    html    latex   example
  psimi25Interactor-class           text    html    latex   example
  psimi25Source-class               text    html    latex   example
  psimi25XML2Graph                  text    html    latex   example
  releaseDate                       text    html    latex   example
  separateXMLDataByExpt             text    html    latex   example
  sourceDb-methods                  text    html    latex
  sourceDb                          text    html    latex
  sourceId-methods                  text    html    latex
  sourceId                          text    html    latex
  taxId-methods                     text    html    latex
  taxId                             text    html    latex   example
  translateID-methods               text    html    latex
  translateID                       text    html    latex   example
  uniprot-methods                   text    html    latex
  uniprot                           text    html    latex   example
  validatePSIMI25                   text    html    latex   example
** building package indices ...
* DONE (RpsiXML)