R Graphical Manual

Browse All

Last data update: 2014.03.03

DiffBind

Package: DiffBind
Type: Package
Version: 2.0.2
Title: Differential Binding Analysis of ChIP-Seq peak data
Author: Rory Stark<rory.stark@cruk.cam.ac.uk>, Gord Brown
<gdbzork@gmail.com>
Maintainer: Rory Stark<rory.stark@cruk.cam.ac.uk>
Description: Compute differentially bound sites from multiple ChIP-seq
experiments using affinity (quantitative) data. Also enables
occupancy (overlap) analysis and plotting functions.
License: Artistic-2.0
LazyLoad: yes
Depends: R (>= 3.3.0), GenomicRanges, SummarizedExperiment
Imports: RColorBrewer, amap, edgeR, gplots, grDevices, limma,
GenomicAlignments, locfit, stats, utils, IRanges, zlibbioc,
lattice, systemPipeR, tools, Rcpp, dplyr, BiocParallel,
parallel, S4Vectors, Rsamtools, DESeq2
Suggests: DESeq, BiocStyle, testthat
Enhances: rgl, XLConnect
LinkingTo: Rsamtools (>= 1.19.38), Rcpp
Collate: core.R parallel.R counts.R contrast.R analyze.R io.R helper.R
utils.R RcppExports.R cpp_wrapper.R DBA.R
biocViews: Sequencing, ChIPSeq, DifferentialPeakCalling
NeedsCompilation: yes
Packaged: 2016-05-18 03:07:15 UTC; biocbuild

● BiocViews: ChIPSeq, DifferentialPeakCalling, Sequencing
● 35 images, 20 functions, 0 datasets
● Reverse Depends: 2

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DiffBind' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c bamReader.cpp -o bamReader.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c bedReader.cpp -o bedReader.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c bitBucket.cpp -o bitBucket.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c croi_func.cpp -o croi_func.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c croi_main.cpp -o croi_main.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c densitySet.cpp -o densitySet.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c iBucket.cpp -o iBucket.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c interval.cpp -o interval.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c intervalDensity.cpp -o intervalDensity.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c intervalNode.cpp -o intervalNode.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c intervalSet.cpp -o intervalSet.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c intervalTree.cpp -o intervalTree.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c merge.cpp -o merge.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c mergeOne.c -o mergeOne.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c nodeGroup.cpp -o nodeGroup.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c peakOrder.cpp -o peakOrder.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c reader.cpp -o reader.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c sequence.cpp -o sequence.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c util.cpp -o util.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o DiffBind.so RcppExports.o bamReader.o bedReader.o bitBucket.o croi_func.o croi_main.o densitySet.o iBucket.o interval.o intervalDensity.o intervalNode.o intervalSet.o intervalTree.o merge.o mergeOne.o nodeGroup.o peakOrder.o reader.o sequence.o util.o /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbam.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbcf.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/DiffBind/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DiffBind'
    finding HTML links ... done
    DiffBind-globals                        html  
    finding level-2 HTML links ... done

    DiffBind-package                        html  
    dba                                     html  
    dba.analyze                             html  
    dba.contrast                            html  
    dba.count                               html  
    dba.load                                html  
    dba.mask                                html  
    dba.overlap                             html  
    dba.peakset                             html  
    dba.plotBox                             html  
    dba.plotHeatmap                         html  
    dba.plotMA                              html  
    dba.plotPCA                             html  
    dba.plotVenn                            html  
    dba.report                              html  
    dba.save                                html  
    dba.show                                html  
    print.DBA                               html  
    tamoxifen                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DiffBind)
Making 'packages.html' ... done