casper

Package: casper
Version: 2.6.0
Date: 2016-02-16
Title: Characterization of Alternative Splicing based on Paired-End
Reads
Author: David Rossell, Camille Stephan-Otto, Manuel Kroiss, Miranda
Stobbe, Victor Pena
Maintainer: David Rossell <rosselldavid@gmail.com>
Depends: R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges
Imports: BiocGenerics, coda, EBarrays, gaga, gtools, GenomeInfoDb,
GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors
(>= 0.9.25), sqldf, survival, VGAM
Enhances: parallel
Description: Infer alternative splicing from paired-end RNA-seq data.
The model is based on counting paths across exons, rather than
pairwise exon connections, and estimates the fragment size and
start distributions non-parametrically, which improves
estimation precision.
License: GPL (>=2)
LazyLoad: yes
Collate: GenericDefs.R ClassDefinitions.R asymmetryCheck.R calcDenovo.R
calcExp.R casperVignettes.R createDenovoGenome.R genePlot.R
getDistrs.R getRoc.R denovoExpr.R makeTranscriptDbFromGFF.R
mergeBatches.R mergeExp.R modelPrior.R pathCounts.R
probNonEquiv.R procBam.R procGenome.R qqnormGenomeWide.R
relexprByGene.R rmShortInserts.R simMultSamples.R simPost.R
simReads.R splitGenomeByLength.R truncnorm.R wrapKnown.R
checks.R wrapDenovo.R
biocViews: GeneExpression, DifferentialExpression, Transcription,
RNASeq, Sequencing
NeedsCompilation: yes
Packaged: 2016-05-04 04:50:15 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'casper' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c casper.cpp -o casper.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cstat.cpp -o cstat.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c dataframe.cpp -o dataframe.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c discretedf.cpp -o discretedf.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c dropVariant.cpp -o dropVariant.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c exon.cpp -o exon.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fragFunc.c -o fragFunc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fragment.cpp -o fragment.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c functions.c -o functions.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hash.c -o hash.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c join_exons.c -o join_exons.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c makeIslands.c -o makeIslands.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c model.cpp -o model.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c model_cmp.cpp -o model_cmp.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pathCounts.c -o pathCounts.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c procBam.c -o procBam.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rcasper.cpp -o rcasper.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c seppel.cpp -o seppel.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c simReads.c -o simReads.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c simReadsfunc.c -o simReadsfunc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c uniqQname.c -o uniqQname.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c variant.cpp -o variant.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c variant_cmp.cpp -o variant_cmp.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/casper/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'transcripts' in package 'casper'
Creating a generic function for 'lines' from package 'graphics' in package 'casper'
** help
*** installing help indices
  converting help for package 'casper'
    finding HTML links ... done
    K562.r1l1                               html  
    annotatedGenome-class                   html  
    asymmetryCheck                          html  
    calcDenovo                              html  
    calcExp                                 html  
    denovoExpr                              html  
    denovoGeneExpr-class                    html  
    denovoGenomeExpr-class                  html  
    distrsGSE37704                          html  
    genePlot                                html  
    getDistrs                               html  
    getIsland                               html  
    getNreads                               html  
    getReads                                html  
    getRoc                                  html  
    hg19DB                                  html  
    mergeBatches                            html  
    mergeExp                                html  
    modelPrior                              html  
    modelPriorAS-class                      html  
    pathCounts-class                        html  
    pathCounts                              html  
    plot-methods                            html  
    plotExpr                                html  
    plotPriorAS                             html  
    probNonEquiv                            html  
    procBam-class                           html  
    procBam                                 html  
    procGenome                              html  
    qqnormGenomeWide                        html  
    quantileNorm                            html  
    relexprByGene                           html  
    rmShortInserts                          html  
    simMAE                                  html  
    simMAEcheck                             html  
    simMultSamples                          html  
    simReads                                html  
    simulatedSamples-class                  html  
    splitGenomeByLength                     html  
    subsetGenome                            html  
    transcripts                             html  
    txLength-methods                        html  
    wrapDenovo                              html  
    wrapKnown                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (casper)
Making 'packages.html' ... done