NMF

Package: NMF
Type: Package
Title: Algorithms and Framework for Nonnegative Matrix Factorization
(NMF)
Version: 0.20.6
Date: 2015-05-25
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Renaud Gaujoux <renaud@tx.technion.ac.il>
Description: Provides a framework to perform Non-negative Matrix
Factorization (NMF). The package implements a set of already published algorithms
and seeding methods, and provides a framework to test, develop and plug
new/custom algorithms. Most of the built-in algorithms have been optimized
in C++, and the main interface function provides an easy way of performing
parallel computations on multicore machines.
License: GPL (>= 2)
URL: http://renozao.github.io/NMF
BugReports: http://github.com/renozao/NMF/issues
SCM: github:renozao, r-forge
LazyLoad: yes
VignetteBuilder: knitr
Depends: R (>= 3.0.0), methods, utils, pkgmaker (>= 0.20), registry,
rngtools (>= 1.2.3), cluster
Imports: graphics, stats, stringr (>= 1.0.0), digest, grid, grDevices,
gridBase, colorspace, RColorBrewer, foreach, doParallel,
ggplot2, reshape2
Suggests: RcppOctave (>= 0.11), fastICA, doMPI, bigmemory (>= 4.2),
synchronicity, corpcor, xtable, devtools, knitr, bibtex, RUnit,
mail, Biobase
Collate: 'rmatrix.R' 'nmf-package.R' 'utils.R' 'versions.R'
'algorithmic.R' 'options.R' 'grid.R' 'colorcode.R' 'atracks.R'
'aheatmap.R' 'NMF-class.R' 'transforms.R' 'Bioc-layer.R'
'NMFstd-class.R' 'NMFOffset-class.R' 'registry.R' 'heatmaps.R'
'NMFns-class.R' 'nmfModel.R' 'fixed-terms.R' 'NMFfit-class.R'
'NMFSet-class.R' 'NMFStrategy-class.R' 'NMFSeed-class.R'
'NMFStrategyFunction-class.R' 'NMFStrategyIterative-class.R'
'NMFStrategyOctave-class.R' 'NMFplots.R'
'registry-algorithms.R' 'algorithms-base.R'
'algorithms-brunet.R' 'algorithms-lnmf.R' 'algorithms-lsnmf.R'
'algorithms-pe-nmf.R' 'algorithms-siNMF.R' 'algorithms-snmf.R'
'data.R' 'extractFeatures.R' 'registry-seed.R' 'parallel.R'
'nmf.R' 'rnmf.R' 'run.R' 'seed-base.R' 'seed-ica.R'
'seed-nndsvd.R' 'setNMFClass.R' 'simulation.R' 'tests.R'
Packaged: 2015-05-25 21:34:47 UTC; renaud
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-05-26 08:12:33

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'NMF' ...
** package 'NMF' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c distance.cpp -o distance.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c divergence.cpp -o divergence.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c euclidean.cpp -o euclidean.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c utils.cpp -o utils.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o NMF.so distance.o divergence.o euclidean.o utils.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/NMF/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Setting package specific options: package:NMF (10 default option(s))
Registering extra action 'Biobase' for handler 'install.packages' ... OK
Creating meta registry in package 'NMF' ... OK
Creating registry 'pkgmaker::extra_action' in package 'NMF' ... OK
Adding entry 'Biobase' in registry 'pkgmaker::extra_action' ... OK
Creating registry 'algorithm' in package 'NMF' ... OK
Registering NMF algorithm '.R#brunet' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'brunet' [NMFStrategyIterative] based on template '.R#brunet' ... OK
Registering NMF algorithm 'KL' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#lee' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'lee' [NMFStrategyIterative] based on template '.R#lee' ... OK
Registering NMF algorithm 'Frobenius' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#offset' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'offset' [NMFStrategyIterative] based on template '.R#offset' ... OK
Registering NMF algorithm '.R#nsNMF' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'nsNMF' [NMFStrategyIterative] based on template '.R#nsNMF' ... OK
Registering NMF algorithm '.M#brunet' [NMFStrategyOctave] ... OK
Registering NMF algorithm 'ls-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'pe-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'snmf/r' [NMFStrategyFunction] ... OK
Registering NMF algorithm 'snmf/l' [NMFStrategyFunction] ... OK
Creating registry 'seed' in package 'NMF' ... OK
Registering extra action 'bigmemory' for handler 'install.packages' ... OK
Adding entry 'bigmemory' in registry 'pkgmaker::extra_action' ... OK
Registering extra action 'synchronicity' for handler 'install.packages' ... OK
Adding entry 'synchronicity' in registry 'pkgmaker::extra_action' ... OK
Registering NMF seeding method 'none' [NMFSeed] ... OK
Registering NMF seeding method 'random' [NMFSeed] ... OK
Registering NMF seeding method 'ica' [NMFSeed] ... OK
Registering NMF seeding method 'nndsvd' [NMFSeed] ... OK
** help
*** installing help indices
  converting help for package 'NMF'
    finding HTML links ... done
    Frobenius-nmf                           html  
    KL-nmf                                  html  
    NMF-class                               html  
    NMF-defunct                             html  
    NMF-deprecated                          html  
    NMF-package                             html  
    NMFList-class                           html  
    NMFOffset-class                         html  
    NMFSeed-class                           html  
    NMFStrategy-class                       html  
    NMFStrategy                             html  
    NMFStrategyFunction-class               html  
    NMFStrategyIterative-class              html  
    NMFStrategyOctave-class                 html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/NMFStrategyOctave-class.Rd:20: missing file link 'RcppOctave'
    NMFfit-class                            html  
    finding level-2 HTML links ... done

    NMFfitX-class                           html  
    NMFfitX                                 html  
    NMFfitX1-class                          html  
    NMFfitXn-class                          html  
    NMFns-class                             html  
    NMFstd-class                            html  
    RNG                                     html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/RNG.Rd:32: missing file link 'getRNG'
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/RNG.Rd:33: missing file link 'getRNG1'
    SNMF-nmf                                html  
    Strategy-class                          html  
    advanced                                html  
    aheatmap                                html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/aheatmap.Rd:24: missing file link 'ExpressionSet-class'
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/aheatmap.Rd:40: missing file link 'display.brewer.all'
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/aheatmap.Rd:228: missing file link 'ExpressionSet-class'
    algorithm-commaNMFList-method           html  
    algorithm-commaNMFStrategyOctave-method
                                            html  
    algorithmic                             html  
    assess                                  html  
    atrack                                  html  
    basis-coef-methods                      html  
    basiscor                                html  
    bioc                                    html  
    c-commaNMF-method                       html  
    canFit                                  html  
    ccBreaks                                html  
    ccPalette                               html  
    ccRamp                                  html  
    ccSpec                                  html  
    checkErrors                             html  
    cluster_mat                             html  
    connectivity                            html  
    consensus-commaNMFfitX1-method          html  
    consensus-commaNMFfitXn-method          html  
    consensushc                             html  
    cophcor                                 html  
    cutdendro                               html  
    deviance                                html  
    dimnames                                html  
    dims                                    html  
    dispersion                              html  
    dot-fcnnls                              html  
    esGolub                                 html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/esGolub.Rd:47: missing file link 'ExpressionSet-class'
    fcnnls                                  html  
    fit                                     html  
    fitted                                  html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/fitted.Rd:62: missing file link 'fitted'
    foreach                                 html  
    gfile                                   html  
    grid                                    html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/grid.Rd:29: missing file link 'current.vpPath'
    heatmaps                                html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/heatmaps.Rd:108: missing file link 'display.brewer.all'
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/heatmaps.Rd:207: missing file link 'ExpressionSet-class'
    inplace                                 html  
    lsNMF-nmf                               html  
    lverbose                                html  
    match_atrack                            html  
    nmf-compare                             html  
    nmf                                     html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/nmf.Rd:451: missing file link 'ExpressionSet'
    nmf.equal                               html  
    nmfAlgorithm                            html  
    nmfApply                                html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/nmfApply.Rd:35: missing file link 'sapply'
    nmfCheck                                html  
    nmfEstimateRank                         html  
    nmfFormals                              html  
    nmfModel                                html  
    nmfObject                               html  
    nmfReport                               html  
    nmfSeed                                 html  
    nmfWrapper                              html  
    nmf_update_KL                           html  
    nmf_update_euclidean                    html  
    nneg                                    html  
    nsNMF-nmf                               html  
    objective-commaNMFfit-method            html  
    offset-commaNMFOffset-method            html  
    offset-commaNMFfit-method               html  
    offset-nmf                              html  
    options                                 html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/options.Rd:50: missing file link 'getOption'
    parallel                                html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/parallel.Rd:57: missing file link 'synchronicity'
    parse_formula                           html  
    plot-commaNMFfit-commamissing-method    html  
    predict                                 html  
    profplot                                html  
    purity                                  html  
    randomize                               html  
    registry-algorithm                      html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/registry-algorithm.Rd:37: missing file link 'pkgreg_fetch'
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/registry-algorithm.Rd:38: missing file link 'pkgreg_remove'
    residuals                               html  
    revPalette                              html  
    rmatrix                                 html  
    rnmf                                    html  
    rss                                     html  
    runtime-commaNMFList-method             html  
    runtime.all-commaNMFfitXn-method        html  
    scale.NMF                               html  
    scores                                  html  
    seed                                    html  
    setNMFMethod                            html  
    setNMFSeed                              html  
Rd warning: /tmp/Rtmp07Xc1v/R.INSTALL3f7f4f2768e0/NMF/man/setNMFSeed.Rd:32: missing file link 'pkgreg_remove'
    setup                                   html  
    show-commaNMF-method                    html  
    show-commaNMFList-method                html  
    show-commaNMFOffset-method              html  
    show-commaNMFSeed-method                html  
    show-commaNMFStrategyIterative-method   html  
    show-commaNMFfit-method                 html  
    show-commaNMFfitX-method                html  
    show-commaNMFfitX1-method               html  
    show-commaNMFfitXn-method               html  
    show-commaNMFns-method                  html  
    silhouette.NMF                          html  
    smoothing                               html  
    sparseness                              html  
    staticVar                               html  
    stop-NMF                                html  
    subset-NMF                              html  
    syntheticNMF                            html  
    t.NMF                                   html  
    terms-internal                          html  
    terms                                   html  
    txtProgressBar                          html  
    types                                   html  
    utils                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NMF)
Making 'packages.html' ... done