adegenet

Package: adegenet
Version: 2.0.1
Encoding: UTF-8
Date: 2016-02-15
Title: Exploratory Analysis of Genetic and Genomic Data
Author: Thibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie-
Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne
Cori, Federico Calboli
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Suggests: pegas, hierfstat, akima, maps, splancs, adehabitat, tripack,
testthat
Depends: R (>= 2.14), methods, ade4
Imports: utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2,
seqinr, parallel, spdep, boot, reshape2, dplyr (>= 0.4.1),
vegan
URL: http://adegenet.r-forge.r-project.org/
Description: Toolset for the exploration of genetic and genomic data. Adegenet
provides formal (S4) classes for storing and handling various genetic data,
including genetic markers with varying ploidy and hierarchical population
structure ('genind' class), alleles counts by populations ('genpop'), and
genome-wide SNP data ('genlight'). It also implements original multivariate
methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance
and similarity measures, and several spatial methods. A range of both empirical
and simulated datasets is also provided to illustrate various methods.
Collate: adegenet.package.R datasets.R orthobasis.R classes.R
constructors.R accessors.R basicMethods.R handling.R auxil.R
minorAllele.R setAs.R SNPbin.R strataMethods.R
hierarchyMethods.R glHandle.R glFunctions.R glSim.R
find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R
chooseCN.R genind2genpop.R loadingplot.R sequences.R
gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R
coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R
xvalDapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R
export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R
simOutbreak.R mutations.R snpposi.R snpzip.R pairDist.R
servers.R zzz.R
License: GPL (>= 2)
LazyLoad: yes
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-02-15 13:36:45 UTC; thibaut
Repository: CRAN
Date/Publication: 2016-02-15 16:12:41

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'adegenet' ...
** package 'adegenet' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GLfunctions.c -o GLfunctions.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c adesub.c -o adesub.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c monmonier-utils.c -o monmonier-utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sharedAll.c -o sharedAll.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c snpbin.c -o snpbin.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o snpbin.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/adegenet/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'adegenet'
Creating a generic function for 'plot' from package 'graphics' in package 'adegenet'
** help
*** installing help indices
  converting help for package 'adegenet'
    finding HTML links ... done
    H3N2                                    html  
    HWE                                     html  
    Hs                                      html  
    Hs.test                                 html  
Rd warning: /tmp/RtmptBc9qp/R.INSTALL4e89319ddea7/adegenet/man/Hs.test.Rd:50: missing file link 'as.randtest'
    SNPbin                                  html  
    accessors                               html  
    adegenet.package                        html  
    as-methods                              html  
    as.SNPbin                               html  
    as.genlight                             html  
    ascore                                  html  
    auxil                                   html  
    chooseCN                                html  
    colorplot                               html  
    coords.monmonier                        html  
    dapc                                    html  
    dapcGraphics                            html  
    dapcIllus                               html  
    df2genind                               html  
    finding level-2 HTML links ... done

    dist.genpop                             html  
    eHGDP                                   html  
    fasta2DNAbin                            html  
    fasta2genlight                          html  
    find.clusters                           html  
    gengraph                                html  
Rd warning: /tmp/RtmptBc9qp/R.INSTALL4e89319ddea7/adegenet/man/gengraph.Rd:19: missing file link 'igraph'
Rd warning: /tmp/RtmptBc9qp/R.INSTALL4e89319ddea7/adegenet/man/gengraph.Rd:96: missing file link 'igraph'
Rd warning: /tmp/RtmptBc9qp/R.INSTALL4e89319ddea7/adegenet/man/gengraph.Rd:104: missing file link 'igraph'
    genind                                  html  
    genind2df                               html  
    genind2genpop                           html  
    genlight                                html  
    genpop                                  html  
    glAux                                   html  
    glPca                                   html  
    glPlot                                  html  
    glSim                                   html  
    haploGen                                html  
    hierarchy-methods                       html  
    hybridize                               html  
    import2genind                           html  
    inbreeding                              html  
    isPoly                                  html  
    loadingplot                             html  
    makefreq                                html  
    microbov                                html  
    minorAllele                             html  
    monmonier                               html  
    mutations                               html  
    nancycats                               html  
    new.genind                              html  
    new.genpop                              html  
    old2new                                 html  
    pairDist                                html  
    population-methods                      html  
    propShared                              html  
    propTyped                               html  
    read.PLINK                              html  
    read.fstat                              html  
    read.genepop                            html  
    read.genetix                            html  
    read.snp                                html  
    read.structure                          html  
    repool                                  html  
    rupica                                  html  
    scaleGen                                html  
    selpopsize                              html  
    seploc                                  html  
    seppop                                  html  
    seqTrack                                html  
    sequences                               html  
    servers                                 html  
    sim2pop                                 html  
    snpposi                                 html  
    snpzip                                  html  
    spca                                    html  
    spca.rtests                             html  
    spcaIllus                               html  
    strata-methods                          html  
    tab                                     html  
    truenames                               html  
    virClasses                              html  
    web                                     html  
    xvalDapc                                html  
** building package indices
** testing if installed package can be loaded
* DONE (adegenet)
Making 'packages.html' ... done