CNPBayes

Package: CNPBayes
Type: Package
Title: Bayesian mixture models for copy number polymorphisms
Version: 1.2.2
Maintainer: Jacob Carey <jcarey15@jhu.edu>
Description: Bayesian hierarchical mixture models for batch effects and copy
number.
Date: Tue Jan 20 20:41:00 EST 2015
Author: Stephen Cristiano, Robert Scharpf, and Jacob Carey
Depends: GenomicRanges
Imports: Rcpp (>= 0.12.1), S4Vectors (>= 0.9.25), matrixStats,
RColorBrewer, gtools, combinat, IRanges, GenomeInfoDb,
GenomicRanges, methods, BiocGenerics, graphics, stats, coda,
SummarizedExperiment
Suggests: testthat, knitr, BiocStyle, VanillaICE (>= 1.31.3),
BiocCheck, MASS, oligoClasses, dplyr, tidyr, ggplot2
Collate: 'help.R' 'AllGenerics.R' 'AllClasses.R' 'RcppExports.R'
'data.R' 'functions.R' 'marginal_likelihood.R'
'methods-BatchModel.R' 'methods-DensityModel.R'
'methods-Hyperparameters.R' 'methods-MarginalModel.R'
'methods-McmcChains.R' 'methods-McmcParams.R'
'methods-MixtureModel.R' 'methods-SummarizedExperiment.R'
'model_initialization.R' 'relabeling.R' 'simulate_data.R'
'visualization.R'
VignetteBuilder: knitr
License: Artistic-2.0
LinkingTo: Rcpp
biocViews: CopyNumberVariation, Bayesian
Roxygen: list(wrap=FALSE)
LazyData: TRUE
URL: https://github.com/scristia/CNPBayes
BugReports: https://github.com/scristia/CNPBayes/issues
NeedsCompilation: yes
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:54:01 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'CNPBayes' ...
** 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 miscfunctions.cpp -o miscfunctions.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 reduced_pooledvariance.cpp -o reduced_pooledvariance.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 singlebatch_pooledvar.cpp -o singlebatch_pooledvar.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 update.cpp -o update.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 updates_batch.cpp -o updates_batch.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 updates_marginal.cpp -o updates_marginal.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 updates_reduced_batch.cpp -o updates_reduced_batch.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 updates_reduced_marginal.cpp -o updates_reduced_marginal.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o CNPBayes.so RcppExports.o miscfunctions.o reduced_pooledvariance.o singlebatch_pooledvar.o update.o updates_batch.o updates_marginal.o updates_reduced_batch.o updates_reduced_marginal.o -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/CNPBayes/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CNPBayes'
    finding HTML links ... done
    BatchModel-class                        html  
    BatchModel                              html  
    BatchModelExample                       html  
    CNPBayes                                html  
    DensityModel-class                      html  
    DensityModel                            html  
    Hyperparameters-class                   html  
    Hyperparameters                         html  
    HyperparametersBatch-class              html  
    HyperparametersBatch                    html  
    HyperparametersMarginal-class           html  
    HyperparametersMarginal                 html  
    MarginalModel-class                     html  
    MarginalModel                           html  
    MarginalModelExample                    html  
    McmcChains-class                        html  
    McmcParams-class                        html  
    McmcParams                              html  
    MixtureModel-class                      html  
    batch-method                            html  
    bic-method                              html  
    burnin-method                           html  
    chains-method                           html  
    chromosome                              html  
    clusters-method                         html  
    collapseBatch-method                    html  
    consensusCNP                            html  
    downSampleEachBatch                     html  
    downsample                              html  
    eta.0-method                            html  
    extract-methods                         html  
    hyperParams-method                      html  
    iter-method                             html  
    k-method                                html  
    labelSwitching-method                   html  
    logBayesFactor                          html  
    logPrior-method                         html  
    log_lik-method                          html  
    m2.0-method                             html  
    map                                     html  
    mapCnProbability                        html  
    marginalLikelihood-method               html  
    mcmcParams-method                       html  
    modes-method                            html  
    mu-method                               html  
    muMean                                  html  
    muc                                     html  
    nStarts-method                          html  
    names-methods                           html  
    nu.0-method                             html  
    oned-method                             html  
    p                                       html  
    pic                                     html  
    plot                                    html  
    posteriorSimulation-method              html  
    posterior_cases                         html  
    probz-method                            html  
    qInverseTau2                            html  
    saveBatch                               html  
    sigma                                   html  
    sigma2-method                           html  
    sigma2.0-method                         html  
    sigmac                                  html  
    simulateBatchData                       html  
    simulateData                            html  
    tau                                     html  
    tau2-method                             html  
    tauMean                                 html  
    tauc                                    html  
    theta-method                            html  
    thin-method                             html  
    tracePlot-method                        html  
    y-method                                html  
    z-method                                html  
    zfreq-method                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNPBayes)
Making 'packages.html' ... done