trackViewer

Package: trackViewer
Type: Package
Title: A bioconductor package with minimalist design for drawing
elegant tracks or lollipop plot
Version: 1.8.4
Date: 2016-06-21
Author: Jianhong Ou, Yong-Xu Wang, Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou@umassmed.edu>
Description: Visualize mapped reads along with annotation as track layers for NGS dataset
such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
License: GPL (>= 2)
Depends: R (>= 3.1.0), methods, GenomicRanges, grid
Imports: GenomicAlignments, GenomicFeatures, Gviz, pbapply, Rsamtools,
rtracklayer, scales, tools, IRanges, AnnotationDbi, grImport
Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocGenerics, BiocStyle, knitr, VariantAnnotation
biocViews: Visualization
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-06-22 04:10:34 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'trackViewer' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'trackViewer'
    finding HTML links ... done
    GRoperator                              html  
    addArrowMark                            html  
    addGuideLine                            html  
    coverageGR                              html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/coverageGR.Rd:8: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/coverageGR.Rd:9: missing file link 'GAlignments'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/coverageGR.Rd:9: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/coverageGR.Rd:25: missing file link 'coverage'
    dandelion.plot                          html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/dandelion.plot.Rd:19: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/dandelion.plot.Rd:19: missing file link 'GRangesList'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/dandelion.plot.Rd:23: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/dandelion.plot.Rd:23: missing file link 'GRangesList'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/dandelion.plot.Rd:26: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/dandelion.plot.Rd:26: missing file link 'GRangesList'
    geneModelFromTxdb                       html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/geneModelFromTxdb.Rd:17: missing file link 'TxDb'
    getCurTrackViewport                     html  
    importBam                               html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/importBam.Rd:15: missing file link 'GRanges'
    importData                              html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/importData.Rd:17: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/importData.Rd:21: missing file link 'RleList'
    importScore                             html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/importScore.Rd:19: missing file link 'GRanges'
    lolliplot                               html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/lolliplot.Rd:17: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/lolliplot.Rd:17: missing file link 'GRangesList'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/lolliplot.Rd:21: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/lolliplot.Rd:21: missing file link 'GRangesList'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/lolliplot.Rd:24: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/lolliplot.Rd:24: missing file link 'GRangesList'
    optimizeStyle                           html  
    parse2GRanges                           html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/parse2GRanges.Rd:19: missing file link 'GRanges'
    parseWIG                                html  
    plotGRanges                             html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/plotGRanges.Rd:16: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/plotGRanges.Rd:17: missing file link 'GRanges'
    pos                                     html  
    track                                   html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/track.rd:29: missing file link 'GRanges'
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/track.rd:31: missing file link 'GRanges'
    trackList                               html  
    trackStyle                              html  
    trackViewer-package                     html  
    trackViewerStyle                        html  
    viewTracks                              html  
Rd warning: /tmp/RtmpB7qfG0/R.INSTALL143d18ecd828/trackViewer/man/viewTracks.Rd:21: missing file link 'GRanges'
    xscale                                  html  
    yaxisStyle                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (trackViewer)
Making 'packages.html' ... done