OrganismDbi

Package: OrganismDbi
Title: Software to enable the smooth interfacing of different database
packages
Description: The package enables a simple unified interface to several
annotation packages each of which has its own schema by taking
advantage of the fact that each of these packages implements a
select methods.
Version: 1.14.1
Author: Marc Carlson, Herve Pages, Martin Morgan, Valerie Obenchain
Maintainer: Biocore Data Team <maintainer@bioconductor.org>
Depends: R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10),
AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.23.31)
Imports: Biobase, BiocInstaller, GenomicRanges, graph, IRanges, RBGL,
RSQLite, S4Vectors (>= 0.9.25), stats
Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19,
AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit
Collate: AllGenerics.R AllClasses.R methods-select.R
methods-transcripts.R createOrganismPackage.R seqinfo.R
test_OrganismDbi_package.R
License: Artistic-2.0
biocViews: Annotation, Infrastructure
NeedsCompilation: no
Packaged: 2016-05-17 03:36:32 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'OrganismDbi' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'OrganismDbi'
    finding HTML links ... done
    OrganismDb                              html  
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/OrganismDb.Rd:191: missing file link 'seqlevels'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/OrganismDb.Rd:192: missing file link 'seqlengths'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/OrganismDb.Rd:193: missing file link 'isCircular'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/OrganismDb.Rd:194: missing file link 'genome'
    coordinate-mapping-method               html  
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/coordinate-mapping-method.Rd:11: missing file link 'mapToAlignments'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/coordinate-mapping-method.Rd:101: missing file link 'mapToTranscripts'
    makeOrganismDbFromBiomart               html  
    finding level-2 HTML links ... done

    makeOrganismDbFromTxDb                  html  
    makeOrganismDbFromUCSC                  html  
    makeOrganismPackage                     html  
    rangeBasedAccessors                     html  
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:93: missing file link 'BSgenome'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:120: missing file link 'GRangesList'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:123: missing file link 'GRangesList'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:125: missing file link 'GRangesList'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:195: missing file link 'GRangesList'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:196: missing file link 'BSgenome'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:197: missing file link 'GRangesList'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:201: missing file link 'DNAString'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:203: missing file link 'Rle'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:206: missing file link 'Rle'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:209: missing file link 'RangesList'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:215: missing file link 'RangesList'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:225: missing file link 'GenomicRanges'
Rd warning: /tmp/RtmpS3NWZO/R.INSTALL663919999643/OrganismDbi/man/rangeBasedAccessors.Rd:253: missing file link 'MultiDb-class'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OrganismDbi)
Making 'packages.html' ... done