GenomicFiles

Package: GenomicFiles
Title: Distributed computing by file or by range
Description: This package provides infrastructure for parallel
computations distributed 'by file' or 'by range'. User
defined MAPPER and REDUCER functions provide added
flexibility for data combination and manipulation.
Version: 1.8.0
Author: Valerie Obenchain, Michael Love, Martin Morgan
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, Coverage
Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges
(>= 1.23.21), SummarizedExperiment, BiocParallel (>= 1.1.0),
Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3)
Imports: GenomicAlignments (>= 1.7.7), Biobase, IRanges, S4Vectors (>=
0.9.25), VariantAnnotation, GenomeInfoDb
Suggests: BiocStyle, RUnit, genefilter, deepSNV,
RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
License: Artistic-2.0
Collate: GenomicFiles-class.R VcfStack-class.R reduceByFile-methods.R
reduceByRange-methods.R reduceFiles.R reduceRanges.R
reduceByYield.R pack-methods.R unpack-methods.R registry.R
zzz.R
Video: https://www.youtube.com/watch?v=3PK_jx44QTs
NeedsCompilation: no
Packaged: 2016-05-04 05:27:40 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenomicFiles' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicFiles'
    finding HTML links ... done
    GenomicFiles-class                      html  
Rd warning: /tmp/Rtmp7OQta4/R.INSTALL59da4eff7d28/GenomicFiles/man/GenomicFiles-class.Rd:110: missing file link 'SummarizedExperiment'
    pack-methods                            html  
    reduceByFile-methods                    html  
    reduceByRange-methods                   html  
    reduceByYield                           html  
Rd warning: /tmp/Rtmp7OQta4/R.INSTALL59da4eff7d28/GenomicFiles/man/reduceByYield.Rd:12: missing file link 'BamFile'
Rd warning: /tmp/Rtmp7OQta4/R.INSTALL59da4eff7d28/GenomicFiles/man/reduceByYield.Rd:29: missing file link 'BamFile'
Rd warning: /tmp/Rtmp7OQta4/R.INSTALL59da4eff7d28/GenomicFiles/man/reduceByYield.Rd:121: missing file link 'BamFile'
Rd warning: /tmp/Rtmp7OQta4/R.INSTALL59da4eff7d28/GenomicFiles/man/reduceByYield.Rd:122: missing file link 'TabixFile'
    registry-utils                          html  
    unpack-methods                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicFiles)
Making 'packages.html' ... done