ToPASeq

Package: ToPASeq
Type: Package
Title: Package for Topology-based Pathway Analysis of RNASeq data
Version: 1.6.0
Date: 2015-12-02
Author: Ivana Ihnatova, Eva Budinska
Maintainer: Ivana Ihnatova <ihnatova@iba.muni.cz>
Description: Implementation of seven methods for topology-based pathway
analysis of both RNASeq and microarray data: SPIA, DEGraph,
TopologyGSA, TAPPA, PRS, PWEA and a visualization tool for a
single pathway.
Depends: graphite (>= 1.16), gRbase, graph, locfit, Rgraphviz
Imports: R.utils, methods, Biobase, parallel, edgeR, DESeq2,
SummarizedExperiment, RBGL, DESeq, fields, limma,
TeachingDemos, KEGGgraph, qpgraph, clipper, AnnotationDbi,
doParallel
Suggests: RUnit, BiocGenerics, gageData, DEGraph, plotrix, org.Hs.eg.db
LinkingTo: Rcpp
LazyData: yes
License: AGPL-3
biocViews: Software, GeneExpression, NetworkEnrichment,
GraphAndNetwork, RNASeq, Visualization, Microarray, Pathways,
DifferentialExpression,
NeedsCompilation: yes
Packaged: 2016-05-04 05:57:10 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ToPASeq' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c accCpp.cpp -o accCpp.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c colMinMax.cpp -o colMinMax.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c downstream.cpp -o downstream.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o ToPASeq.so RcppExports.o accCpp.o colMinMax.o downstream.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/ToPASeq/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'numNoEdges' from package 'graph' in package 'ToPASeq'
Creating a generic function for 'mostEdges' from package 'graph' in package 'ToPASeq'
** help
*** installing help indices
  converting help for package 'ToPASeq'
    finding HTML links ... done
    AdjacencyMatrix2Pathway                 html  
    Clipper                                 html  
    DEGraph                                 html  
    Deprecated                              html  
    KEGG2pathway                            html  
    PRS                                     html  
    PWEA                                    html  
    SPIA                                    html  
    TAPPA                                   html  
    ToPASeq-package                         html  
    TopologyGSA                             html  
    collectWeightsPRS                       html  
    convertIdentifiersByVector              html  
    defaultEdgeAttrs                        html  
    estimateCF                              html  
    graphNEL2Pathway                        html  
    pathway-class                           html  
    preparePathways                         html  
    reduceRraph                             html  
    res                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ToPASeq)
Making 'packages.html' ... done