methylPipe

Package: methylPipe
Type: Package
Title: Base resolution DNA methylation data analysis
Version: 1.6.2
Date: 2016-03-16
Author: Kamal Kishore
Maintainer: Kamal Kishore <kamal.fartiyal84@gmail.com>
Description: Memory efficient analysis of base resolution DNA methylation data in both
the CpG and non-CpG sequence context. Integration of DNA methylation data derived from
any methodology providing base- or low-resolution data.
License: GPL(>=2)
LazyLoad: yes
Imports: marray, gplots, IRanges, BiocGenerics, Gviz,
GenomicAlignments, Biostrings, parallel, data.table,
GenomeInfoDb, S4Vectors
Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils,
GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools
Suggests: BSgenome.Hsapiens.UCSC.hg18,
TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR
VignetteBuilder: knitr
biocViews: MethylSeq, DNAMethylation, Coverage, Sequencing
NeedsCompilation: yes
Packaged: 2016-05-16 04:49:45 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'methylPipe' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_methylPipe.c -o R_init_methylPipe.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c binning.c -o binning.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o methylPipe.so R_init_methylPipe.o binning.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/methylPipe/libs
** R
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'methylPipe'
    finding HTML links ... done
    BSdata-class                            html  
    finding level-2 HTML links ... done

    BSdataSet-class                         html  
    BSprepare                               html  
    GEcollection-class                      html  
    GElist-class                            html  
    chiCombP                                html  
    consolidateDMRs                         html  
    extractBinGRanges                       html  
    findDMR                                 html  
    findPMDs                                html  
    getCpos                                 html  
    getCposDensity                          html  
    mCsmoothing                             html  
    mapBSdata2GRanges                       html  
    meth.call                               html  
    methstats                               html  
    methylPipe-package                      html  
    plotMeth                                html  
    pool.reads                              html  
    process.hmc                             html  
    profileDNAmetBin                        html  
    splitChrs                               html  
    tabixdata2GR                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methylPipe)
Making 'packages.html' ... done