hapFabia

Package: hapFabia
Title: hapFabia: Identification of very short segments of identity by
descent (IBD) characterized by rare variants in large
sequencing data
Version: 1.14.0
Date: 2014-06-20
Author: Sepp Hochreiter <hochreit@bioinf.jku.at>
Maintainer: Sepp Hochreiter <hochreit@bioinf.jku.at>
Depends: R (>= 2.12.0), Biobase, fabia (>= 2.3.1)
Imports: methods, graphics, grDevices, stats, utils
LinkingTo:
Description: A package to identify very short IBD segments in large
sequencing data by FABIA biclustering. Two haplotypes are
identical by descent (IBD) if they share a segment that both
inherited from a common ancestor. Current IBD methods reliably
detect long IBD segments because many minor alleles in the
segment are concordant between the two haplotypes. However,
many cohort studies contain unrelated individuals which share
only short IBD segments. This package provides software to
identify short IBD segments in sequencing data. Knowledge of
short IBD segments are relevant for phasing of genotyping data,
association studies, and for population genetics, where they
shed light on the evolutionary history of humans. The package
supports VCF formats, is based on sparse matrix operations, and
provides visualization of haplotype clusters in different
formats.
License: LGPL (>= 2.1)
Collate: AllClasses.R AllGenerics.R hapFabia.R
methods-Factorization-class.R methods-IBDsegment-class.R
methods-IBDsegmentList-class.R zzz.R
URL: http://www.bioinf.jku.at/software/hapFabia/hapFabia.html
biocViews: Genetics, GeneticVariability, SNP, Sequencing, Sequencing,
Visualization, Clustering, SequenceMatching, Software
NeedsCompilation: yes
Packaged: 2016-05-04 04:42:42 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'hapFabia' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c interfaceR.c -o interfaceR.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/ddbj/local/lib64/R/lib -lR
gcc -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 
gcc -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 
gcc ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
gcc -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 
gcc -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 
gcc ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/ddbj/local/lib64/R/library/hapFabia/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'hapFabia'
    finding HTML links ... done
    IBDsegment-class                        html  
    IBDsegmentList-class                    html  
    IBDsegmentList2excel                    html  
    analyzeIBDsegments                      html  
    chr1ASW1000G                            html  
    compareIBDsegmentLists                  html  
    extractIBDsegments                      html  
    findDenseRegions                        html  
    hapFabia                                html  
    hapFabiaVersion                         html  
    hapRes                                  html  
    identifyDuplicates                      html  
    iterateIntervals                        html  
    makePipelineFile                        html  
    matrixPlot                              html  
    mergeIBDsegmentLists                    html  
    mergedIBDsegmentList                    html  
    plotIBDsegment                          html  
    res                                     html  
    setAnnotation                           html  
    setStatistics                           html  
    sim                                     html  
    simu                                    html  
    simulateIBDsegments                     html  
    simulateIBDsegmentsFabia                html  
    split_sparse_matrix                     html  
    toolsFactorizationClass                 html  
    vcftoFABIA                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hapFabia)
Making 'packages.html' ... done