diffHic

Package: diffHic
Version: 1.4.2
Date: 2016-06-14
Title: Differential Analyis of Hi-C Data
Author: Aaron Lun <alun@wehi.edu.au>
Maintainer: Aaron Lun <alun@wehi.edu.au>
Depends: R (>= 3.3.0), GenomicRanges, InteractionSet,
SummarizedExperiment
Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma,
csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb,
BiocGenerics, grDevices, graphics, stats, utils
Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix
biocViews: MultipleComparison, Preprocessing, Sequencing, Coverage,
Alignment, Normalization, Clustering, HiC
Description: Detects differential interactions across biological
conditions in a Hi-C experiment. Methods are provided for read
alignment and data pre-processing into interaction counts.
Statistical analysis is based on edgeR and supports
normalization and filtering. Several visualization options are
also available.
License: GPL-3
NeedsCompilation: yes
LinkingTo: Rhtslib, zlibbioc
Packaged: 2016-06-15 05:18:26 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'diffHic' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c binner.cpp -o binner.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c check_input.cpp -o check_input.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c cluster_2d.cpp -o cluster_2d.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c count_background.cpp -o count_background.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c count_connect.cpp -o count_connect.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c count_patch.cpp -o count_patch.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c directionality.cpp -o directionality.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c init.cpp -o init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c iterative_correction.cpp -o iterative_correction.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c nb_average.cpp -o nb_average.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c neighbors.cpp -o neighbors.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c pair_stats.cpp -o pair_stats.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c quadrant_bg.cpp -o quadrant_bg.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c report_hic_pairs.cpp -o report_hic_pairs.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include" -I"/home/ddbj/local/lib64/R/library/zlibbioc/include"   -fpic  -g -O2  -c trended_filter.cpp -o trended_filter.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o diffHic.so binner.o check_input.o cluster_2d.o count_background.o count_connect.o count_patch.o directionality.o init.o iterative_correction.o nb_average.o neighbors.o pair_stats.o quadrant_bg.o report_hic_pairs.o trended_filter.o -L/home/ddbj/local/lib64/R/library/Rhtslib/lib -Wl,-rpath,/home/ddbj/local/lib64/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/diffHic/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'diffHic'
    finding HTML links ... done
    DIList                                  html  
    DNaseHiC                                html  
    annotatePairs                           html  
    finding level-2 HTML links ... done

    boxPairs                                html  
    clusterPairs                            html  
    compartmentalize                        html  
    connectCounts                           html  
Rd warning: /tmp/Rtmpdq1Kxi/R.INSTALL1cfd3cd47e5f/diffHic/man/connectCounts.Rd:74: missing file link 'ReverseStrictGInteractions-class'
    consolidatePairs                        html  
    correctedContact                        html  
    cutGenome                               html  
    diClusters                              html  
    diffHicUsersGuide                       html  
    domainDirections                        html  
    enrichedPairs                           html  
    filterDiag                              html  
Rd warning: /tmp/Rtmpdq1Kxi/R.INSTALL1cfd3cd47e5f/diffHic/man/filterDiag.Rd:43: missing file link 'pairdist'
    filterPeaks                             html  
    filters                                 html  
    getArea                                 html  
    getDistance                             html  
    getPairData                             html  
    loadData                                html  
    marginCounts                            html  
    mergePairs                              html  
    neighborCounts                          html  
    normalizeCNV                            html  
    pairParam                               html  
    plotDI                                  html  
    plotPlaid                               html  
    preparePairs                            html  
    prunePairs                              html  
    savePairs                               html  
    squareCounts                            html  
Rd warning: /tmp/Rtmpdq1Kxi/R.INSTALL1cfd3cd47e5f/diffHic/man/squareCounts.Rd:101: missing file link 'ReverseStrictGInteractions-class'
    totalCounts                             html  
    wrappers                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffHic)
Making 'packages.html' ... done