Last data update: 2014.03.03
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RpsiXML
Package: RpsiXML
Version: 2.14.0
Date: 2015-04-09
Title: R interface to PSI-MI 2.5 files
Author: Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase,
RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2),
AnnotationDbi
Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db,
org.Sc.sgd.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db,
hom.Rn.inp.db, hom.Sc.inp.db, Rgraphviz, ppiStats, ScISI
Description: Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.
Collate: AllClasses.R AllGenerics.R AllMethods.R SAXhandlers.R
funcsAnnotation.R hyperGraphs.R psi25parser.R psimi25Source.R
validatePSIMI25.R graphSpeciesConverter.R
License: LGPL-3
URL: http://www.bioconductor.org
biocViews: Infrastructure, Proteomics
NeedsCompilation: no
Packaged: 2016-05-04 03:09:44 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'RpsiXML' ...
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
Note: in method for 'head' with signature 'x="ANY"': expanding the
signature to include omitted arguments in definition: x = "missing"
Note: in method for 'tail' with signature 'x="ANY"': expanding the
signature to include omitted arguments in definition: x = "missing"
** help
*** installing help indices
converting help for package 'RpsiXML'
finding HTML links ... done
BIOGRID.PSIMI25 html
availableXrefs-methods html
availableXrefs html
bait html
buildPCHypergraph html
complexName html
complexes html
eListHandler html
getAbstractByPMID html
graphSpeciesConverter html
interactionType html
interactions html
interactorInfo-methods html
interactorInfo html
interactors html
list2Matrix html
null2na html
numInteractions-methods html
parsePsimi25Interaction html
psimi25Attribute-class html
psimi25Complex-class html
psimi25ComplexEntry-class html
psimi25Experiment-class html
psimi25Graph-class html
psimi25Hypergraph-class html
psimi25Hypergraph2GraphNEL html
psimi25Interaction-class html
psimi25InteractionEntry-class html
psimi25Interactor-class html
psimi25Source-class html
psimi25XML2Graph html
separateXMLDataByExpt html
sourceId-methods html
taxId-methods html
translateID-methods html
translateID html
uniprot-methods html
uniprot html
validatePSIMI25 html
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* DONE (RpsiXML)
Making 'packages.html' ... done
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