kebabs

Package: kebabs
Type: Package
Title: Kernel-Based Analysis Of Biological Sequences
Version: 1.6.2
Date: 2016-04-28
Author: Johannes Palme
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Description: The package provides functionality for kernel-based analysis of
DNA, RNA, and amino acid sequences via SVM-based methods. As core
functionality, kebabs implements following sequence kernels:
spectrum kernel, mismatch kernel, gappy pair kernel, and
motif kernel. Apart from an efficient implementation of standard
position-independent functionality, the kernels are extended in a
novel way to take the position of patterns into account for the
similarity measure. Because of the flexibility of the kernel
formulation, other kernels like the weighted degree kernel or
the shifted weighted degree kernel with constant weighting of
positions are included as special cases. An annotation-specific
variant of the kernels uses annotation information placed along
the sequence together with the patterns in the sequence.
The package allows for the generation of a kernel matrix or an
explicit feature representation in dense or sparse format for all
available kernels which can be used with methods implemented in
other R packages. With focus on SVM-based methods, kebabs
provides a framework which simplifies the usage of existing
SVM implementations in kernlab, e1071, and LiblineaR. Binary and
multi-class classification as well as regression tasks can be used
in a unified way without having to deal with the different
functions, parameters, and formats of the selected SVM. As support
for choosing hyperparameters, the package provides cross
validation - including grouped cross validation, grid search and
model selection functions. For easier biological interpretation of
the results, the package computes feature weights for all SVMs and
prediction profiles which show the contribution of individual
sequence positions to the prediction result and indicate the
relevance of sequence sections for the learning result and the
underlying biological functions.
URL: http://www.bioinf.jku.at/software/kebabs/
##Roxygen: list(wrap=TRUE)
License: GPL (>= 2.1)
Collate: AllClasses.R AllGenerics.R access-methods.R svmModel.R
kebabs.R kebabsData.R runtimeMessage.R parameters.R
sequenceKernel.R annotationSpecificKernel.R
positionDependentKernel.R spectrum.R mismatch.R gappyPair.R
motif.R explicitRepresentation.R coerce-methods.R
featureWeights.R heatmap-methods.R kbsvm-methods.R
performCrossValidation-methods.R gridSearch.R modelSelection.R
trainsvm-methods.R predictsvm-methods.R predict-methods.R
predictionProfile.R plot-methods.R kebabsDemo.R show-methods.R
symmetricPair.R svm.R utils.R zzz.R
Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab
Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
utils, apcluster
LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors
Suggests: SparseM, Biobase, BiocGenerics, knitr
VignetteBuilder: knitr
biocViews: SupportVectorMachine, Classification, Clustering, Regression
Packaged: 2016-05-16 05:07:15 UTC; biocbuild
NeedsCompilation: yes

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'kebabs' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c ByteStringVector.c -o ByteStringVector.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c GappyPairC.cpp -o GappyPairC.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c KernelUtils.cpp -o KernelUtils.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c MismatchC.cpp -o MismatchC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c MotifC.cpp -o MotifC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c PredictionC.cpp -o PredictionC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c Rsvm.c -o Rsvm.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c SpectrumC.cpp -o SpectrumC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c Utils.cpp -o Utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include" -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/S4Vectors/include"   -fpic  -g -O2  -c svm.cpp -o svm.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/kebabs/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'kebabs'
    finding HTML links ... done
    BioVector-class                         html  
    finding level-2 HTML links ... done

    BioVector                               html  
    ControlInformation-class                html  
    CrossValidationResult-class             html  
    CrossValidationResultAccessors          html  
    ExplicitRepresentation-class            html  
    ExplicitRepresentationAccessors         html  
    GappyPairKernel-class                   html  
    KBModel-class                           html  
    KBModelAccessors                        html  
    KernelMatrix-class                      html  
    KernelMatrixAccessors                   html  
    LinearKernel                            html  
    MismatchKernel-class                    html  
    ModelSelectionResult-class              html  
    ModelSelectionResultAccessors           html  
    MotifKernel-class                       html  
    PredictionProfile-class                 html  
    PredictionProfileAccessors              html  
    ROCData-class                           html  
    ROCDataAccessors                        html  
    SVMAccess                               html  
    SVMInformation-class                    html  
    SequenceKernel-class                    html  
    SpectrumKernel-class                    html  
    SymmetricPairKernel-class               html  
    annotationSpecificKernel                html  
    computeROCandAUC                        html  
    evaluatePrediction                      html  
    explicitRepresentation                  html  
    featureWeights                          html  
    gappyPairKernel                         html  
    genRandBioSeqs                          html  
    getPredProfMixture-methods              html  
    getPredictionProfile-methods            html  
    heatmap-methods                         html  
    kbsvm-methods                           html  
    kebabsCollectInfo                       html  
    kebabsData                              html  
    kebabsOverview                          html  
    mismatchKernel                          html  
    motifKernel                             html  
    performCrossValidation-methods          html  
    performGridSearch                       html  
    performModelSelection                   html  
    plot-methods                            html  
    positionDependentKernel                 html  
    predict-methods                         html  
    sequenceKernel                          html  
    show-methods                            html  
    spectrumKernel                          html  
    symmetricPairKernel                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (kebabs)
Making 'packages.html' ... done