strataG

Package: strataG
Title: Summaries and Population Structure Analyses of Genetic Data
Description: A toolkit for analyzing stratified population genetic data.
Version: 1.0.5
License: GNU General Public License
Authors@R: c(
EA = person("Eric", "Archer", email = "eric.archer@noaa.gov", role = c("aut", "cre")),
PA = person("Paula", "Adams", email = "peadams@crimson.ua.edu", role = c("aut")),
BS = person("Brita", "Schneiders", email = "britaschneiders@u.northwestern.edu", role = c("aut")))
BugReports: https://github.com/EricArcher/strataG/issues
Depends: R (>= 3.2.0), apex, adegenet
Suggests: knitr, rmarkdown
Imports: ape, copula, ggplot2, graphics, Hmisc, methods, pegas,
phangorn, RColorBrewer, Rcpp, reshape2, stats, swfscMisc, utils
Collate: strataG-package.R gtypes.class.R gtypes.accessors.R
is.gtypes.R initialize.gtypes.R strataG-internal.R
as.matrix.gtypes.R as.data.frame.gtypes.R alleleFreqFormat.R
alleleFreqs.R alleleSplit.R allelicRichness.R as.multidna.R
baseFreqs.R clumpp.R createConsensus.R dupGenotypes.R evanno.R
expectedNumAlleles.R fasta.R fastsimcoal.input.R fastsimcoal.R
fixedDifferences.R fixedSites.R freq2GenData.R fstToNm.R
fusFs.R gelato.R genepop.R haplotypeLikelihoods.R
heterozygosity.R Hstats.R hweTest.R idRows.R iupacCode.R
jackHWE.R labelHaplotypes.R LDgenepop.R lowFreqSubs.R mRatio.R
mafft.R mega.R mostDistantSequences.R
mostRepresentativeSequences.R neiDa.R nucleotideDivergence.R
nucleotideDiversity.R numAlleles.R numGensEq.R numMissing.R
permuteStrata.R phase.R popStructStat.R popStructTest.R
privateAlleles.R propUniqueAlleles.R qaqc.R RcppExports.R
readGenData.R removeSequences.R sharedLoci.R show.gtypes.R
simGammaHaps.R statChi2.R statFis.R statFst.R statGst.R
statJostD.R statPhist.R strataSplit.R stratify.R structure.R
structurePlot.R summarizeLoci.R summarizeSeqs.R
summary.gtypes.R tajimasD.R theta.R TiTvRatio.R trimNs.R
validIupacCodes.R variableSites.R wrightFst.R write.arlequin.R
write.gtypes.R write.nexus.snapp.R gtypes2genind.R
gtypes2loci.R df2gtypes.R sequence2gtypes.R gtypes2phyDat.R
LazyData: true
VignetteBuilder: knitr
LinkingTo: Rcpp
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-30 22:38:19 UTC; eric.archer
Author: Eric Archer [aut, cre],
Paula Adams [aut],
Brita Schneiders [aut]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Repository: CRAN
Date/Publication: 2016-05-31 07:51:52

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'strataG' ...
** package 'strataG' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c Hstats_C.cpp -o Hstats_C.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c misc.funcs.cpp -o misc.funcs.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c statChi2_C.cpp -o statChi2_C.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c statFis_C.cpp -o statFis_C.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c statFst_C.cpp -o statFst_C.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c statGst_C.cpp -o statGst_C.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c statJostD_C.cpp -o statJostD_C.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c statPhist_C.cpp -o statPhist_C.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o strataG.so Hstats_C.o RcppExports.o misc.funcs.o statChi2_C.o statFis_C.o statFst_C.o statGst_C.o statJostD_C.o statPhist_C.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/strataG/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'as.data.frame' from package 'base' in package 'strataG'
** help
*** installing help indices
  converting help for package 'strataG'
    finding HTML links ... done
    LDgenepop                               html  
    TiTvRatio                               html  
    alleleFreqFormat                        html  
    alleleFreqs                             html  
    alleleSplit                             html  
    allelicRichness                         html  
    as.data.frame.gtypes                    html  
Rd warning: /tmp/RtmpF8RHzS/R.INSTALL129365f1ce0b/strataG/man/as.data.frame.gtypes.Rd:54: missing file link 'as.matrix'
    as.matrix-gtypes-method                 html  
Rd warning: /tmp/RtmpF8RHzS/R.INSTALL129365f1ce0b/strataG/man/as.matrix-gtypes-method.Rd:54: missing file link 'as.data.frame'
    as.multidna                             html  
    finding level-2 HTML links ... done

    baseFreqs                               html  
    bowhead.snp.position                    html  
    bowhead.snps                            html  
    clumpp                                  html  
    createConsensus                         html  
    df2gtypes                               html  
    dloop.g                                 html  
    dolph.haps                              html  
    dolph.msats                             html  
    dolph.seqs                              html  
    dolph.strata                            html  
    dupGenotypes                            html  
    evanno                                  html  
    expectedNumAlleles                      html  
    fasta                                   html  
    fastsimcoal                             html  
    fastsimcoal.input                       html  
    fixedDifferences                        html  
    fixedSites                              html  
    freq2GenData                            html  
    fstToNm                                 html  
    fusFs                                   html  
    gelato                                  html  
    genepop                                 html  
    gtypes-class                            html  
    gtypes.accessors                        html  
Rd warning: /tmp/RtmpF8RHzS/R.INSTALL129365f1ce0b/strataG/man/gtypes.accessors.Rd:141: missing file link 'getSequences'
    gtypes2genind                           html  
    gtypes2loci                             html  
Rd warning: /tmp/RtmpF8RHzS/R.INSTALL129365f1ce0b/strataG/man/gtypes2loci.Rd:18: missing file link 'loci'
    gtypes2phyDat                           html  
    haplotypeLikelihoods                    html  
    heterozygosity                          html  
    hweTest                                 html  
    idRows                                  html  
    initialize-gtypes-method                html  
    is.gtypes                               html  
    iupacCode                               html  
    jackHWE                                 html  
    labelHaplotypes                         html  
    lowFreqSubs                             html  
    mRatio                                  html  
    mafft                                   html  
    mega                                    html  
    mostDistantSequences                    html  
    mostRepresentativeSequences             html  
    msats.g                                 html  
    neiDa                                   html  
    nucleotideDivergence                    html  
    nucleotideDiversity                     html  
    numAlleles                              html  
    numGensEq                               html  
    numMissing                              html  
    permuteStrata                           html  
    phase                                   html  
    popStructStat                           html  
    popStructTest                           html  
    privateAlleles                          html  
    propUniqueAlleles                       html  
    qaqc                                    html  
    readGenData                             html  
    removeSequences                         html  
    sequence2gtypes                         html  
    sharedLoci                              html  
    show-gtypes-method                      html  
    simGammaHaps                            html  
    strataG-internal                        html  
    strataG-package                         html  
    strataSplit                             html  
    stratify                                html  
    structure                               html  
    structurePlot                           html  
    summarizeLoci                           html  
    summarizeSeqs                           html  
    summary-gtypes-method                   html  
    tajimasD                                html  
    theta                                   html  
    trimNs                                  html  
    validIupacCodes                         html  
    variableSites                           html  
    wrightFst                               html  
    write.arlequin                          html  
    write.gtypes                            html  
Rd warning: /tmp/RtmpF8RHzS/R.INSTALL129365f1ce0b/strataG/man/write.gtypes.Rd:28: missing file link 'as.matrix'
    write.nexus.snapp                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (strataG)
Making 'packages.html' ... done