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Last data update: 2014.03.03
GenABEL

Package: GenABEL
Type: Package
Title: genome-wide SNP association analysis
Version: 1.8-0
Date: 2013-12-09
Author: GenABEL project developers
Contact: GenABEL project developers <genabel.project at gmail.com>
Maintainer: Yurii Aulchenko <yurii@bionet.nsc.ru>
Depends: R (>= 2.15.0), methods, MASS, utils, GenABEL.data
Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm,
MetABEL, PredictABEL, VariABEL, bigRR
Description: a package for genome-wide association analysis between
quantitative or binary traits and single-nucleotide
polymorphisms (SNPs).
License: GPL (>= 2)
URL: http://www.genabel.org
http://genabel.r-forge.r-project.org/
BugReports: http://r-forge.r-project.org/tracker/?group_id=505
Packaged: 2013-12-26 05:48:08 UTC; maksim
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-12-27 14:47:02
● Cran Task View: Genetics
● 41 images, 115 functions, 0 datasets
● Reverse Depends: 3
Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenABEL' ...
** package 'GenABEL' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c AbstractMatrix.cpp -o AbstractMatrix.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c AbstractMatrix_R.cpp -o AbstractMatrix_R.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c CastUtils.cpp -o CastUtils.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c Chip.cpp -o Chip.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c FileVector.cpp -o FileVector.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c FilteredMatrix.cpp -o FilteredMatrix.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c FilteredMatrix_R.cpp -o FilteredMatrix_R.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c Logger.cpp -o Logger.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c RealHandlerWrapper.cpp -o RealHandlerWrapper.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c ReusableFileHandle.cpp -o ReusableFileHandle.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c Transposer.cpp -o Transposer.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c chinv2.cpp -o chinv2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c cholesky2.cpp -o cholesky2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c chsolve2.cpp -o chsolve2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c convert.snp.affymetrix.cpp -o convert.snp.affymetrix.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c convert_snp_illumina.cpp -o convert_snp_illumina.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c convert_snp_merlin.cpp -o convert_snp_merlin.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c convert_snp_merlin_wslash.cpp -o convert_snp_merlin_wslash.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c convert_snp_tped.cpp -o convert_snp_tped.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c convert_util.cpp -o convert_util.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c coxfit2.cpp -o coxfit2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c dautil.cpp -o dautil.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c dmatrix.cpp -o dmatrix.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c dometa.cpp -o dometa.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c export_plink.cpp -o export_plink.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fexact.c -o fexact.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c frutil.cpp -o frutil.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c gtps_container.cpp -o gtps_container.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gwaa.c -o gwaa.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c gwaa_cpp.cpp -o gwaa_cpp.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c gwaa_data.cpp -o gwaa_data.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c gwaautil.cpp -o gwaautil.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c interactions_rare_recesive_alleles.cpp -o interactions_rare_recesive_alleles.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c iterator.cpp -o iterator.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c iterator_functions.cpp -o iterator_functions.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c lm_gwaa.cpp -o lm_gwaa.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2  -c merge.snp.data.cpp -o merge.snp.data.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o GenABEL.so AbstractMatrix.o AbstractMatrix_R.o CastUtils.o Chip.o FileVector.o FilteredMatrix.o FilteredMatrix_R.o Logger.o RealHandlerWrapper.o ReusableFileHandle.o Transposer.o chinv2.o cholesky2.o chsolve2.o convert.snp.affymetrix.o convert_snp_illumina.o convert_snp_merlin.o convert_snp_merlin_wslash.o convert_snp_tped.o convert_util.o coxfit2.o dautil.o dmatrix.o dometa.o export_plink.o fexact.o frutil.o gtps_container.o gwaa.o gwaa_cpp.o gwaa_data.o gwaautil.o interactions_rare_recesive_alleles.o iterator.o iterator_functions.o lm_gwaa.o merge.snp.data.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/GenABEL/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenABEL'
    finding HTML links ... done
    GASurv                                  html  
    GenABEL                                 html  
    HWE.show                                html  
    PGC                                     html  
    VIFGC                                   html  
    VIFGC_ovdom                             html  
    Xfix                                    html  
    add.phdata                              html  
    add.plot                                html  
    arrange_probabel_phe                    html  
    as.character.gwaa.data                  html  
    as.character.snp.coding                 html  
    as.character.snp.data                   html  
    as.character.snp.strand                 html  
    as.data.frame.gwaa.data                 html  
    as.double.gwaa.data                     html  
    as.double.snp.data                      html  
    as.genotype                             html  
    as.genotype.gwaa.data                   html  
    as.genotype.snp.data                    html  
    as.hsgeno                               html  
    as.hsgeno.gwaa.data                     html  
    as.hsgeno.snp.data                      html  
    autosomal                               html  
    blurGenotype                            html  
    catable                                 html  
    ccfast                                  html  
    check.marker-class                      html  
    check.marker                            html  
    check.trait                             html  
    checkPackageVersionOnCRAN               html  
    cocohet                                 html  
    convert.snp.affymetrix                  html  
    convert.snp.illumina                    html  
    convert.snp.mach                        html  
    convert.snp.ped                         html  
    convert.snp.text                        html  
    convert.snp.tped                        html  
    crnames                                 html  
    del.phdata                              html  
    descriptives.marker                     html  
    descriptives.scan                       html  
    descriptives.trait                      html  
    dprfast                                 html  
    egscore                                 html  
    egscore.old                             html  
    emp.ccfast                              html  
    emp.qtscore                             html  
    estlambda                               html  
    export.impute                           html  
    export.merlin                           html  
    export.plink                            html  
    extract.annotation.impute               html  
    extract.annotation.mach                 html  
    findRelatives                           html  
    formetascore                            html  
    generateOffspring                       html  
    getLogLikelihoodGivenRelation           html  
    grammar                                 html  
    gwaa.data-class                         html  
    hom                                     html  
    hom.old                                 html  
    ibs                                     html  
    ibs.old                                 html  
    impute2databel                          html  
    impute2mach                             html  
    load.gwaa.data                          html  
    mach2databel                            html  
    makeTransitionMatrix                    html  
    merge.gwaa.data                         html  
    merge.snp.data                          html  
    mlreg                                   html  
    mlreg.p                                 html  
    mmscore                                 html  
    npsubtreated                            html  
    patch_strand                            html  
    perid.summary                           html  
    plot.check.marker                       html  
    plot.scan.gwaa.2D                       html  
    plot.scan.gwaa                          html  
    polygenic                               html  
    polygenic_hglm                          html  
    qtscore                                 html  
    qvaluebh95                              html  
    r2fast                                  html  
    r2fast.old                              html  
    recodeChromosome                        html  
    reconstructNPs                          html  
    redundant                               html  
    refresh.gwaa.data                       html  
    rhofast                                 html  
    rntransform                             html  
    save.gwaa.data                          html  
    scan.glm.2D                             html  
    scan.glm                                html  
    scan.gwaa-class                         html  
    scan.gwaa.2D-class                      html  
    scan.haplo.2D                           html  
    scan.haplo                              html  
    show.ncbi                               html  
    snp.coding-class                        html  
    snp.data-class                          html  
    snp.data                                html  
    snp.mx-class                            html  
    snp.names                               html  
    snp.strand-class                        html  
    snp.subset                              html  
    snps.cell-class                         html  
    sortmap.internal                        html  
    sset                                    html  
    summary.check.marker                    html  
    summary.gwaa.data                       html  
    summary.scan.gwaa                       html  
    summary.snp.data                        html  
    ztransform                              html  
** building package indices
** testing if installed package can be loaded
* DONE (GenABEL)
Making 'packages.html' ... done