csaw

Package: csaw
Version: 1.6.1
Date: 2016-03-12
Title: ChIP-Seq Analysis with Windows
Author: Aaron Lun <alun@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>
Maintainer: Aaron Lun <alun@wehi.edu.au>
Depends: R (>= 3.3.0), GenomicRanges, SummarizedExperiment (>= 1.1.6)
Imports: Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi,
methods, S4Vectors, IRanges, GenomeInfoDb, BiocGenerics,
Rhtslib, stats
Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene
biocViews: MultipleComparison, ChIPSeq, Normalization, Sequencing,
Coverage, Genetics, Annotation, DifferentialPeakCalling
Description: Detection of differentially bound regions in ChIP-seq data
with sliding windows, with methods for normalization and proper
FDR control.
License: GPL-3
NeedsCompilation: yes
LinkingTo: Rhtslib, zlibbioc
Packaged: 2016-05-26 04:56:29 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'csaw' ...
** 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 annotator.cpp -o annotator.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 bam_utils.cpp -o bam_utils.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 best_in_cluster.cpp -o best_in_cluster.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_bimodality.cpp -o check_bimodality.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 correlate_reads.cpp -o correlate_reads.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 find_maxima.cpp -o find_maxima.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 get_cluster_stats.cpp -o get_cluster_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 get_profile.cpp -o get_profile.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 get_rle_counts.cpp -o get_rle_counts.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 merge_windows.cpp -o merge_windows.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_reads.cpp -o pair_reads.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 single_reads.cpp -o single_reads.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.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/csaw/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'csaw'
    finding HTML links ... done
    SEmethods                               html  
    finding level-2 HTML links ... done

    checkBimodality                         html  
    clusterFDR                              html  
    clusterWindows                          html  
    combineTests                            html  
    consolidateClusters                     html  
    consolidateSizes                        html  
    correlateReads                          html  
    csawUsersGuide                          html  
    detailRanges                            html  
    extractReads                            html  
    filterWindows                           html  
    findMaxima                              html  
    getBestTest                             html  
    getPESizes                              html  
    getWidths                               html  
    maximizeCcf                             html  
    mergeWindows                            html  
    normOffsets                             html  
    overlapStats                            html  
    paramList                               html  
    profileSites                            html  
    readParam                               html  
    regionCounts                            html  
    scaledAverage                           html  
    strandedCounts                          html  
    upweightSummit                          html  
    windowCounts                            html  
    wwhm                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (csaw)
Making 'packages.html' ... done