genoset

Package: genoset
Type: Package
Title: A RangedSummarizedExperiment with methods for copy number
analysis
Version: 1.28.2
Date: 2016-04-12
Author: Peter M. Haverty
Maintainer: Peter M. Haverty <phaverty@gene.com>
Description: GenoSet provides an extension of the RangedSummarizedExperiment class
with additional API
features. This class provides convenient and fast methods for working with
segmented genomic data. Additionally,
GenoSet provides the class RleDataFrame which stores runs of data along the
genome for multiple samples and provides very fast summaries of arbitrary
row sets (regions of the genome).
License: Artistic-2.0
LazyLoad: yes
Depends: R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>=
1.17.19), SummarizedExperiment (>= 1.1.6)
Imports: S4Vectors (>= 0.9.25), GenomeInfoDb (>= 1.1.3), IRanges (>=
2.5.12), methods, graphics
Suggests: RUnit, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome,
Biostrings
Enhances: parallel
ByteCompile: TRUE
biocViews: Infrastructure, DataRepresentation, Microarray, SNP,
CopyNumberVariation
Collate: 'genoset-class.R' 'RleDataFrame-class.R'
'RleDataFrame-methods.R' 'bounds.R' 'deprecated.R' 'ordering.R'
'plots.R' 'rangeSummaries.R' 'segments.R'
'test_genoset_package.R' 'utils.R' 'zzz.R'
VignetteBuilder: knitr
URL: https://github.com/phaverty/genoset
Packaged: 2016-05-16 02:50:56 UTC; biocbuild
RoxygenNote: 5.0.1
NeedsCompilation: yes

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'genoset' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bounds.c -o bounds.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rangeSummaries.c -o rangeSummaries.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c utils.c -o utils.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o genoset.so bounds.o init.o rangeSummaries.o utils.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'colMeans' in package 'genoset'
Creating a new generic function for 'colSums' in package 'genoset'
Creating a new generic function for 'rowMeans' in package 'genoset'
Creating a new generic function for 'rowSums' in package 'genoset'
** help
*** installing help indices
  converting help for package 'genoset'
    finding HTML links ... done
    GenoSet-class                           html  
    finding level-2 HTML links ... done

    RleDataFrame-class                      html  
    RleDataFrame-views                      html  
    baf2mbaf                                html  
    boundingIndices                         html  
    boundingIndicesByChr                    html  
    bounds2Rle                              html  
    calcGC                                  html  
    calcGC2                                 html  
    chr-methods                             html  
    chrIndices-methods                      html  
    chrInfo-methods                         html  
    chrNames-methods                        html  
    chrOrder                                html  
    chrPartitioning                         html  
    cn2lr-methods                           html  
    do_rledf_range_summary                  html  
    do_rledf_views                          html  
    fixSegNAs                               html  
    gcCorrect                               html  
    genoPlot-methods                        html  
    genoPos-methods                         html  
    genome                                  html  
    genomeAxis                              html  
    genomicranges-methods                   html  
    genoset-dataset                         html  
    genoset-methods                         html  
    genoset-package                         html  
    genoset-subset                          html  
    isGenomeOrder-methods                   html  
    lr2cn                                   html  
    modeCenter                              html  
    numCallable                             html  
    pos-methods                             html  
    rangeSampleMeans                        html  
    rangeSegMeanLength-methods              html  
    rbindDataframe                          html  
    readGenoSet                             html  
    runCBS                                  html  
    segPairTable-methods                    html  
    segTable-methods                        html  
    segs2Granges                            html  
    segs2Rle                                html  
    segs2RleDataFrame                       html  
    toGenomeOrder                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for 'colMeans'
Warning: multiple methods tables found for 'colSums'
Warning: multiple methods tables found for 'rowMeans'
Warning: multiple methods tables found for 'rowSums'
* DONE (genoset)
Making 'packages.html' ... done