pcaMethods

Package: pcaMethods
Maintainer: Henning Redestig <henning.red@gmail.com>
License: GPL (>= 3)
Title: A collection of PCA methods
LinkingTo: Rcpp
LazyLoad: Yes
Author: Wolfram Stacklies, Henning Redestig, Kevin Wright
SystemRequirements: Rcpp
Description: Provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
Inverse Non-Linear PCA and the conventional SVD PCA. A cluster
based method for missing value estimation is included for
comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA
on incomplete data as well as for accurate missing value
estimation. A set of methods for printing and plotting the
results is also provided. All PCA methods make use of the same
data structure (pcaRes) to provide a common interface to the
PCA results. Initiated at the Max-Planck Institute for
Molecular Plant Physiology, Golm, Germany.
Version: 1.64.0
URL: https://github.com/hredestig/pcamethods
BugReports: https://github.com/hredestig/pcamethods/issues
Depends: Biobase, methods
Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS
Suggests: matrixStats, lattice, ggplot2
Collate: 'derrorHierarchic.R' 'errorHierarchic.R' 'AllClasses.R'
'AllGenerics.R' 'BPCA_dostep.R' 'BPCA_initmodel.R' 'bpca.R'
'checkData.R' 'forkNlpcaNet.R' 'kEstimate.R' 'kEstimateFast.R'
'lineSearch.R' 'llsImpute.R' 'methods-ExpressionSet.R'
'methods-nniRes.R' 'methods-pcaRes.R' 'nipalsPca.R' 'nlpca.R'
'optiAlgCgd.R' 'orth.R' 'pca.R' 'pcaMethods-package.R' 'ppca.R'
'prep.R' 'repmat.R' 'robustPca.R' 'sortFeatures.R'
'svdImpute.R' 'vector2matrices.R' 'xval.R'
Packaged: 2016-05-04 02:56:16 UTC; biocbuild
biocViews: Bayesian
RoxygenNote: 5.0.1
NeedsCompilation: yes

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'pcaMethods' ...
** 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 nipals.cpp -o nipals.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o pcaMethods.so RcppExports.o nipals.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/pcaMethods/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'loadings' in package 'pcaMethods'
Creating a generic function for 'print' from package 'base' in package 'pcaMethods'
Creating a generic function for 'biplot' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'summary' from package 'base' in package 'pcaMethods'
Creating a generic function for 'predict' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'resid' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'fitted' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'plot' from package 'graphics' in package 'pcaMethods'
** help
*** installing help indices
  converting help for package 'pcaMethods'
    finding HTML links ... done
    BPCA_dostep                             html  
    BPCA_initmodel                          html  
    DModX-pcaRes-method                     html  
    Q2                                      html  
    R2VX-pcaRes-method                      html  
    R2cum-pcaRes-method                     html  
    RnipalsPca                              html  
    asExprSet                               html  
    biplot-methods                          html  
    bpca                                    html  
    center-pcaRes-method                    html  
    centered-pcaRes-method                  html  
    checkData                               html  
    completeObs-nniRes-method               html  
    cvseg                                   html  
    cvstat-pcaRes-method                    html  
    deletediagonals                         html  
    derrorHierarchic                        html  
    dim.pcaRes                              html  
    errorHierarchic                         html  
    fitted-methods                          html  
    forkNlpcaNet                            html  
    getHierarchicIdx                        html  
    helix                                   html  
    kEstimate                               html  
    kEstimateFast                           html  
    leverage-pcaRes-method                  html  
    lineSearch                              html  
    linr                                    html  
    listPcaMethods                          html  
    llsImpute                               html  
    loadings-ANY-method                     html  
    loadings-pcaRes-method                  html  
    loadings.pcaRes                         html  
    metaboliteData                          html  
    metaboliteDataComplete                  html  
    method-pcaRes-method                    html  
    nObs-pcaRes-method                      html  
    nP-pcaRes-method                        html  
    nPcs-pcaRes-method                      html  
    nVar-pcaRes-method                      html  
    nipalsPca                               html  
    nlpca                                   html  
    nmissing-pcaRes-method                  html  
    nni                                     html  
    nniRes                                  html  
    optiAlgCgd                              html  
    orth                                    html  
    pca                                     html  
    pcaMethods-deprecated                   html  
    pcaMethods                              html  
    pcaNet                                  html  
    pcaRes                                  html  
    plot.pcaRes                             html  
    plotPcs                                 html  
    ppca                                    html  
    predict-methods                         html  
    prep                                    html  
    rediduals-methods                       html  
    repmat                                  html  
    robustPca                               html  
    robustSvd                               html  
    sDev-pcaRes-method                      html  
    scaled-pcaRes-method                    html  
    scl-pcaRes-method                       html  
    scores-pcaRes-method                    html  
    scores.pcaRes                           html  
    show-methods                            html  
    showNniRes                              html  
    simpleEllipse                           html  
    slplot-pcaRes-method                    html  
    sortFeatures                            html  
    summary                                 html  
    svdImpute                               html  
    svdPca                                  html  
    tempFixNas                              html  
    vector2matrices-matrix-method           html  
    vector2matrices-nlpcaNet-method         html  
    wasna-pcaRes-method                     html  
    weightsAccount                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pcaMethods)
Making 'packages.html' ... done