InteractionSet

Package: InteractionSet
Version: 1.0.4
Date: 2016-06-14
Title: Base Classes for Storing Genomic Interaction Data
Author: Aaron Lun <alun@wehi.edu.au>, Malcolm Perry <mgperry32@gmail.com>,
Liz Ing-Simmons <liz.ing-simmons12@csc.mrc.ac.uk>
Maintainer: Aaron Lun <alun@wehi.edu.au>
Depends: R (>= 3.3.0), GenomicRanges, SummarizedExperiment (>= 1.1.6)
Imports: IRanges, S4Vectors (>= 0.9.24), GenomeInfoDb, BiocGenerics,
methods, Matrix
Suggests: testthat, knitr, rmarkdown, BiocStyle
biocViews: Infrastructure, DataRepresentation, Software, HiC
Description: Provides the GInteractions, InteractionSet and ContactMatrix
objects and associated methods for storing and manipulating genomic
interaction data from Hi-C and ChIA-PET experiments.
License: GPL-3
NeedsCompilation: yes
VignetteBuilder: knitr
Collate: ContactMatrix-class.R GInteractions-class.R
InteractionSet-class.R getset.R matching.R swapAnchors.R
GRanges-methods.R pairs.R conversion.R linearize.R
boundingBox.R distances.R overlaps.R linkOverlaps.R
Packaged: 2016-06-15 06:02:09 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'InteractionSet' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c box_bounds.cpp -o box_bounds.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.cpp -o init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c overlaps.cpp -o overlaps.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o InteractionSet.so box_bounds.o init.o overlaps.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/InteractionSet/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'InteractionSet'
    finding HTML links ... done
    ContactMatrix-accessors                 html  
    finding level-2 HTML links ... done

    ContactMatrix-class                     html  
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/ContactMatrix-class.Rd:42: missing file link 'Annotated'
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/ContactMatrix-class.Rd:51: missing file link 'Annotated'
    ContactMatrix-distances                 html  
    ContactMatrix-overlaps                  html  
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/ContactMatrix-overlaps.Rd:33: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/ContactMatrix-overlaps.Rd:37: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/ContactMatrix-overlaps.Rd:100: missing file link 'findOverlaps'
    ContactMatrix-sorting                   html  
    ContactMatrix-subset                    html  
    GInteractions-class                     html  
    InteractionSet-class                    html  
    boundingBox                             html  
    conversion                              html  
    distances                               html  
    granges-methods                         html  
    interaction-accessors                   html  
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/interaction-accessors.Rd:126: missing file link 'mcols'
    interaction-compare                     html  
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/interaction-compare.Rd:214: missing file link 'pcompare'
    interaction-subset                      html  
    linearize                               html  
    linkOverlaps                            html  
    overlaps                                html  
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/overlaps.Rd:99: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/overlaps.Rd:103: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/overlaps.Rd:132: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpIy68Uo/R.INSTALL59ff3ed1d271/InteractionSet/man/overlaps.Rd:238: missing file link 'findOverlaps'
    pairs                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (InteractionSet)
Making 'packages.html' ... done