DESeq2

Package: DESeq2
Type: Package
Title: Differential gene expression analysis based on the negative
binomial distribution
Version: 1.12.3
Author: Michael Love (HSPH Boston), Simon Anders, Wolfgang Huber (EMBL
Heidelberg)
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
Description: Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution.
License: LGPL (>= 3)
VignetteBuilder: knitr
Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,
methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)
Depends: S4Vectors (>= 0.9.25), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
Suggests: testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer,
airway, IHW, tximport, tximportData, readr, pasilla (>=
0.2.10), DESeq
LinkingTo: Rcpp, RcppArmadillo
biocViews: Sequencing, ChIPSeq, RNASeq, SAGE, DifferentialExpression,
GeneExpression, Transcription
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-26 03:48:34 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DESeq2' ...
** 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/RcppArmadillo/include"   -fpic  -g -O2  -c DESeq2.cpp -o DESeq2.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/RcppArmadillo/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o DESeq2.so DESeq2.o RcppExports.o -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DESeq2'
    finding HTML links ... done
    DESeq                                   html  
    finding level-2 HTML links ... done

    DESeq2-package                          html  
    DESeqDataSet                            html  
    DESeqResults                            html  
    DESeqTransform                          html  
    coef                                    html  
    collapseReplicates                      html  
    counts                                  html  
    design                                  html  
    dispersionFunction                      html  
    dispersions                             html  
    estimateBetaPriorVar                    html  
    estimateDispersions                     html  
    estimateDispersionsGeneEst              html  
    estimateSizeFactors                     html  
    estimateSizeFactorsForMatrix            html  
    fpkm                                    html  
    fpm                                     html  
    makeExampleDESeqDataSet                 html  
    nbinomLRT                               html  
    nbinomWaldTest                          html  
    normTransform                           html  
    normalizationFactors                    html  
    normalizeGeneLength                     html  
    plotCounts                              html  
    plotDispEsts                            html  
    plotMA                                  html  
    plotPCA                                 html  
    plotSparsity                            html  
    replaceOutliers                         html  
    results                                 html  
Rd warning: /tmp/RtmplxuYKT/R.INSTALL618a72c17f62/DESeq2/man/results.Rd:320: missing file link 'filtered_R'
    rlog                                    html  
    show                                    html  
    sizeFactors                             html  
    summary                                 html  
    varianceStabilizingTransformation       html  
    vst                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)
Making 'packages.html' ... done