GenomeInfoDb

Package: GenomeInfoDb
Title: Utilities for manipulating chromosome and other 'seqname'
identifiers
Description: Contains data and functions that
define and allow translation between different chromosome
sequence naming conventions (e.g., "chr1" versus "1"),
including a function that attempts to place sequence names in
their natural, rather than lexicographic, order.
Version: 1.8.1
Author: Sonali Arora, Martin Morgan, Marc Carlson, H. Pages
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, DataRepresentation, Annotation, GenomeAnnotation
Depends: R (>= 3.1), methods, stats4, BiocGenerics (>= 0.13.8),
S4Vectors (>= 0.9.25), IRanges (>= 1.99.26)
Imports: methods, BiocGenerics, S4Vectors
Suggests: GenomicRanges, Rsamtools, GenomicAlignments, BSgenome,
GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
License: Artistic-2.0
Collate: utils.R rankSeqlevels.R assembly-utils.R taxIDSpeciesLookup.R
fetchExtendedChromInfoFromUCSC.R fetchSequenceInfo.R seqinfo.R
seqlevelsStyle.R seqlevels-wrappers.R Seqinfo-class.R
GenomeDescription-class.R zzz.R
VignetteBuilder: knitr
Video: http://youtu.be/wdEjCYSXa7w
NeedsCompilation: no
Packaged: 2016-05-12 04:19:39 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenomeInfoDb' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomeInfoDb'
    finding HTML links ... done
    GenomeDescription-class                 html  
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/GenomeDescription-class.Rd:45: missing file link 'BSgenome'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/GenomeDescription-class.Rd:46: missing file link 'BSgenome'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/GenomeDescription-class.Rd:126: missing file link 'BSgenome'
    Seqinfo-class                           html  
    availableSpecies                        html  
    fetchExtendedChromInfoFromUCSC          html  
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/fetchExtendedChromInfoFromUCSC.Rd:130: missing file link 'getBSgenome'
    rankSeqlevels                           html  
    seqinfo                                 html  
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:79: missing file link 'GRanges'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:94: missing file link 'GRangesList'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:95: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:96: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:144: missing file link 'GRanges'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:144: missing file link 'GRangesList'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:145: file link 'SummarizedExperiment' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:147: missing file link 'GAlignments'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:148: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:149: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:151: missing file link 'TxDb'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:153: missing file link 'BSgenome'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:188: missing file link 'GRanges'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:188: missing file link 'GRangesList'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:189: file link 'SummarizedExperiment' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:192: missing file link 'GAlignments'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:193: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:194: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:197: missing file link 'TxDb'
Rd warning: /tmp/RtmpcuaLZp/R.INSTALL5c101f1ce363/GenomeInfoDb/man/seqinfo.Rd:200: missing file link 'BSgenome'
    seqlevels-wrappers                      html  
    seqlevelsStyle                          html  
    speciesMap                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomeInfoDb)
Making 'packages.html' ... done