biovizBase

Package: biovizBase
Version: 1.20.0
Title: Basic graphic utilities for visualization of genomic data.
Description: The biovizBase package is designed to provide a set of
utilities, color schemes and conventions for genomic data. It
serves as the base for various high-level packages for
biological data visualization. This saves development effort
and encourages consistency.
Authors@R: c(person("Tengfei", "Yin", role=c("aut"),
email="yintengfei@gmail.com"),
person("Michael", "Lawrence", role=c("aut", "ths", "cre"),
email="lawrence.michael@gene.com"),
person("Dianne", "Cook", role=c("aut", "ths")),
person("Johannes", "Rainer", role="ctb"))
Depends: R (>= 2.10), methods
Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,
BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 1.99.28),
GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),
SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=
1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=
1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),
ensembldb (>= 1.3.8)
Suggests: BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,
EnsDb.Hsapiens.v75, RUnit
License: Artistic-2.0
LazyLoad: Yes
Collate: utils.R color.R AllGenerics.R crunch-method.R mold-method.R
addStepping-method.R getFragLength-method.R
shrinkageFun-method.R maxGap-method.R spliceSummary-method.R
ideogram.R pileup.R coverage.R labs.R original.R transform.R
facets-method.R aes.R scale.R zzz.R biovizBase-package.R
biocViews: Infrastructure, Visualization, Preprocessing
NeedsCompilation: yes
Packaged: 2016-05-04 04:13:45 UTC; biocbuild
Author: Tengfei Yin [aut],
Michael Lawrence [aut, ths, cre],
Dianne Cook [aut, ths],
Johannes Rainer [ctb]
Maintainer: Michael Lawrence <lawrence.michael@gene.com>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'biovizBase' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bin_offsets.c -o bin_offsets.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'biovizBase'
    finding HTML links ... done
    CRC                                     html  
    GCcontent                               html  
    addStepping-method                      html  
    aes-utils                               html  
    biovizBase-package                      html  
    colorBlindSafePal                       html  
    containLetters                          html  
    crc1.GeRL                               html  
    crunch-method                           html  
Rd warning: /tmp/Rtmp3zLfxo/R.INSTALL6604156028c4/biovizBase/man/crunch-method.Rd:31: missing file link 'BasicFilter-class'
    darned_hg19_subset500                   html  
    estimateCoverage-method                 html  
    flatGrl                                 html  
    genesymbol                              html  
    getBioColor                             html  
    getFormalNames                          html  
    getGaps                                 html  
    getIdeoGR                               html  
    getIdeogram                             html  
    getScale                                html  
    hg19Ideogram                            html  
    hg19IdeogramCyto                        html  
    ideo                                    html  
    ideoCyto                                html  
    isIdeogram                              html  
    isMatchedWithModel                      html  
    isSimpleIdeogram                        html  
    labs                                    html  
    maxGap-method                           html  
    mold-method                             html  
    finding level-2 HTML links ... done

    pileupAsGRanges                         html  
    pileupGRangesAsVariantTable             html  
    plotColorLegend                         html  
    scale                                   html  
    showColor                               html  
    shrinkageFun-method                     html  
    splitByFacets-method                    html  
    strip_formula_dots                      html  
    subsetArgsByFormals                     html  
    transform                               html  
    transformGRangesForEvenSpace            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biovizBase)
Making 'packages.html' ... done