contiBAIT

Package: contiBAIT
Type: Package
Title: Improves Early Build Genome Assemblies using Strand-Seq Data
Version: 1.0.0
Date: 2016-02-02
Author: Kieran O'Neill, Mark Hills, Mike Gottlieb
Maintainer: Kieran O'Neill <koneill@bccrc.ca>
Description: Using strand inheritance data from multiple single cells
from the organism whose genome is to be assembled, contiBAIT
can cluster unbridged contigs together into putative
chromosomes, and order the contigs within those chromosomes.
License: BSD_2_clause + file LICENSE
Depends: BH (>= 1.51.0-3), Rsamtools (>= 1.21)
LinkingTo: Rcpp, BH
Imports: grDevices, clue, cluster, gplots, IRanges, GenomicRanges,
S4Vectors, Rcpp, TSP, GenomicFiles, gtools, rtracklayer,
BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods,
exomeCopy, diagram
Suggests: BiocStyle
biocViews: CellBasedAssays, QualityControl, WholeGenome, Genetics,
GenomeAssembly
Collate: 'AllClasses.R' 'AllGenerics.R' 'BAIT.R'
'barplotLinkageGroupCalls.R' 'clusterContigs.R'
'computeConsensus.R' 'computeSim.R' 'contiBAIT.R'
'ideogramPlot.R' 'makeBoxPlot.R' 'makeChrTable.R'
'mapGapFromOverlap.R' 'mergeLinkageGroups.R'
'orderAllLinkageGroups.R' 'orderContigsGreedy.R'
'orderContigsTSP.R' 'plotContigOrder.R' 'plotLGDistances.R'
'plotWCdistribution.R' 'preprocessStrandTable.R'
'reorientLinkageGroups.R' 'strandSeqFreqTable.R' 'writeBed.R'
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-04 06:48:07 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'contiBAIT' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2  -c computeSim.cpp -o computeSim.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o contiBAIT.so computeSim.o orderContigsGreedy.o -lm -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/contiBAIT/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'contiBAIT'
    finding HTML links ... done
    BAIT                                    html  
    ChrTable                                html  
    ContigOrdering                          html  
    LinkageGroupList                        html  
    OrientationFrame                        html  
    StrandFreqMatrix                        html  
    StrandReadMatrix                        html  
    StrandStateMatrix                       html  
    barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
                                            html  
    clusterContigs-StrandStateMatrix-method
                                            html  
    contiBAIT                               html  
    exampleChrTable                         html  
    exampleCrickFreq                        html  
    exampleDividedChr                       html  
    exampleLGList                           html  
    exampleReadCounts                       html  
    exampleStrandFreq                       html  
    exampleWCMatrix                         html  
    exampleWatsonFreq                       html  
    ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
                                            html  
    makeBoxPlot                             html  
    makeChrTable                            html  
    mapGapFromOverlap                       html  
    mergeLinkageGroups                      html  
    orderAllLinkageGroups                   html  
    orderContigsGreedy                      html  
    orderContigsTSP                         html  
    plotContigOrder                         html  
    plotLGDistances-LinkageGroupList-StrandStateMatrix-method
                                            html  
    plotWCdistribution-StrandFreqMatrix-method
                                            html  
    preprocessStrandTable-StrandFreqMatrix-method
                                            html  
    reorientLinkageGroups                   html  
    show-ContigOrdering-method              html  
    show-LinkageGroupList-method            html  
    show-OrientationFrame-method            html  
    show-StrandFreqMatrix-method            html  
    show-StrandReadMatrix-method            html  
    show-StrandStateMatrix-method           html  
    strandSeqFreqTable                      html  
    writeBed                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (contiBAIT)
Making 'packages.html' ... done