ensembldb

Package: ensembldb
Type: Package
Title: Utilities to create and use an Ensembl based annotation database
Version: 1.4.6
Author: Johannes Rainer <johannes.rainer@eurac.edu>,
Tim Triche <tim.triche@usc.edu>
Maintainer: Johannes Rainer <johannes.rainer@eurac.edu>
URL: https://github.com/jotsetung/ensembldb
BugReports: https://github.com/jotsetung/ensembldb/issues
Imports: methods, RSQLite, DBI, Biobase, GenomeInfoDb, AnnotationDbi
(>= 1.31.19), rtracklayer, S4Vectors, AnnotationHub, Rsamtools,
IRanges
Depends: BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.23.21),
GenomicFeatures (>= 1.23.18)
Suggests: BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75 (>= 0.99.7),
RUnit, shiny, Gviz, BSgenome.Hsapiens.UCSC.hg19
VignetteBuilder: knitr
Description: The package provides functions to create and use
transcript centric annotation databases/packages. The
annotation for the databases are directly fetched from Ensembl
using their Perl API. The functionality and data is similar to
that of the TxDb packages from the GenomicFeatures package,
but, in addition to retrieve all gene/transcript models and
annotations from the database, the ensembldb package provides
also a filter framework allowing to retrieve annotations for
specific entries like genes encoded on a chromosome region or
transcript models of lincRNA genes.
Collate: Classes.R Generics.R dbhelpers.R Methods.R Methods-Filter.R
loadEnsDb.R makeEnsemblDbPackage.R EnsDbFromGTF.R runEnsDbApp.R
select-methods.R seqname-utils.R zzz.R
biocViews: Genetics, AnnotationData, Sequencing, Coverage
License: LGPL
NeedsCompilation: no
Packaged: 2016-06-07 05:12:18 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ensembldb' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'transcriptLengths' in package 'ensembldb'
** help
*** installing help indices
  converting help for package 'ensembldb'
    finding HTML links ... done
    EnsDb-AnnotationDbi                     html  
Rd warning: /tmp/RtmpFEepWD/R.INSTALL65db3921ee73/ensembldb/man/EnsDb-AnnotationDbi.Rd:72: missing file link 'mapIds'
    EnsDb-class                             html  
    EnsDb-exonsBy                           html  
Rd warning: /tmp/RtmpFEepWD/R.INSTALL65db3921ee73/ensembldb/man/EnsDb-exonsBy.Rd:146: missing file link 'exonsByOverlaps'
Rd warning: /tmp/RtmpFEepWD/R.INSTALL65db3921ee73/ensembldb/man/EnsDb-exonsBy.Rd:152: missing file link 'exonsByOverlaps'
Rd warning: /tmp/RtmpFEepWD/R.INSTALL65db3921ee73/ensembldb/man/EnsDb-exonsBy.Rd:183: missing file link 'exonsByOverlaps'
Rd warning: /tmp/RtmpFEepWD/R.INSTALL65db3921ee73/ensembldb/man/EnsDb-exonsBy.Rd:232: missing file link 'exonsByOverlaps'
    EnsDb-lengths                           html  
    EnsDb-seqlevels                         html  
    EnsDb-sequences                         html  
    EnsDb-utils                             html  
    GeneidFilter-class                      html  
    SeqendFilter                            html  
    makeEnsemblDbPackage                    html  
    runEnsDbApp                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ensembldb)
Making 'packages.html' ... done