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 |
* 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
* 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)