oligoClasses

Package: oligoClasses
Version: 1.34.0
Title: Classes for high-throughput arrays supported by oligo and crlmm
Author: Benilton Carvalho and Robert Scharpf
Maintainer: Benilton Carvalho <beniltoncarvalho@gmail.com> and Robert Scharpf <rscharpf@jhsph.edu>
Depends: R (>= 2.14)
Imports: BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), methods,
graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7),
SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>=
1.23.2), ff, foreach, BiocInstaller, utils, S4Vectors (>=
0.9.25), RSQLite
Enhances: doMC, doMPI, doSNOW, doParallel, doRedis
Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6,
pd.genomewidesnp.5, pd.mapping50k.hind240,
pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp,
genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6),
RUnit, human370v1cCrlmm, SNPchip, VanillaICE, crlmm
Description: This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
License: GPL (>= 2)
LazyLoad: yes
Collate: AllClasses.R AllGenerics.R utils-general.R utils-lds.R
utils-parallel.R methods-gSet.R initialize-methods.R
methods-AlleleSet.R methods-AnnotatedDataFrame.R
methods-FeatureSet.R methods-AssayData.R
methods-SnpFeatureSet.R methods-oligoSnpSet.R
methods-CopyNumberSet.R methods-CNSet.R methods-PDInfo.R
methods-RangedDataCNV.R methods-SnpSet.R
methods-GenomeAnnotatedDataFrame.R methods-BeadStudioSet.R
methods-BeadStudioSetList.R methods-gSetList.R
methods-GRanges.R methods-SummarizedExperiment.R show-methods.R
functions.R zzz.R
biocViews: Infrastructure
## Local Variables:
## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
## End:
NeedsCompilation: no
Packaged: 2016-05-04 03:02:22 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'oligoClasses' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'oligoClasses'
Creating a generic function for 'close' from package 'base' in package 'oligoClasses'
** help
*** installing help indices
  converting help for package 'oligoClasses'
    finding HTML links ... done
    AlleleSet-class                         html  
    finding level-2 HTML links ... done

    AlleleSet-methods                       html  
    AssayData-methods                       html  
    AssayDataList                           html  
    BeadStudioSet-class                     html  
    BeadStudioSetList-class                 html  
    CNSet-class                             html  
    ClassesNotExported                      html  
    CopyNumberSet-class                     html  
    CopyNumberSet-methods                   html  
    DBPDInfo-class                          html  
    FeatureSetExtensions-class              html  
    GRanges-methods                         html  
    GenomeAnnotatedDataFrame-class          html  
    GenomeAnnotatedDataFrameFrom-methods    html  
    SnpSet-methods                          html  
    SnpSet2-class                           html  
    SnpSuperSet-class                       html  
    SummarizedExperiment-methods            html  
    affyPlatforms                           html  
    annotationPackages                      html  
    assayDataList-methods                   html  
    batch                                   html  
    batchStatistics                         html  
    celfileDate                             html  
    celfileName                             html  
    checkExists                             html  
    checkOrder                              html  
    chromosome-methods                      html  
    chromosome2integer                      html  
    clusterOpts                             html  
    clusterOptsDeprecated                   html  
    createFF                                html  
    data-efsExample                         html  
    data-scqsExample                        html  
    data-sfsExample                         html  
    data-sqsExample                         html  
    db                                      html  
    defunct                                 html  
    exprs-methods                           html  
    featureDataList-methods                 html  
    ff_matrix                               html  
    ff_or_matrix-class                      html  
    ffdf                                    html  
    fileConnections                         html  
    flags                                   html  
    gSet-class                              html  
    gSetList-class                          html  
    generics                                html  
    genomeBuild                             html  
    geometry-methods                        html  
    getBar                                  html  
    getSequenceLengths                      html  
    i2p_p2i                                 html  
    integerMatrix                           html  
    is.ffmatrix                             html  
    isPackageLoaded                         html  
    isSnp-methods                           html  
    kind                                    html  
    largeObjects                            html  
    ldOpts                                  html  
    length-methods                          html  
    library2                                html  
    list.celfiles                           html  
    locusLevelData                          html  
    makeFeatureGRanges                      html  
    manufacturer-methods                    html  
    ocLapply                                html  
    oligoSetExample                         html  
    oligoSnpSet-methods                     html  
    parStatus                               html  
    pdPkgFromBioC                           html  
    platform-methods                        html  
    pmFragmentLength-methods                html  
    position-methods                        html  
    requireAnnotation                       html  
    requireClusterPkgSetDeprecated          html  
    sampleNames-methods                     html  
    splitVec                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligoClasses)
Making 'packages.html' ... done