poppr

Package: poppr
Type: Package
Title: Genetic Analysis of Populations with Mixed Reproduction
Version: 2.2.0
Date: 2016-06-08
Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
email = "kamvarz@science.oregonstate.edu"),
person(c("Javier", "F."), "Tabima", role = "aut",
email = "tabimaj@onid.orst.edu"),
person(c("Sydney", "E."), "Everhart", role = c("ctb", "dtc"),
email = "everhart@unl.edu"),
person(c("Jonah", "C."), "Brooks", role = "aut",
email = "brookjon@onid.orst.edu"),
person(c("Stacy", "A."), "Krueger-Hadfield", role = "ctb",
email = "kruegersa@cofc.edu"),
person(c("Erik"), "Sotka", role = "ctb",
email = "sotkae@cofc.edu"),
person(c("Brian", "J."), "Knaus", role = "ctb",
email = "briank.lists@gmail.com"),
person(c("Niklaus", "J."), "Grunwald", role = "ths",
email = "grunwaln@science.oregonstate.edu"))
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Encoding: UTF-8
URL: http://github.com/grunwaldlab/poppr
http://grunwaldlab.github.io/Population_Genetics_in_R/,
http://grunwaldlab.cgrb.oregonstate.edu/poppr-r-package-population-genetics
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
MailingList: http://groups.google.com/group/poppr
BugReports: https://github.com/grunwaldlab/poppr/issues
Depends: R (>= 2.15.1), adegenet (>= 2.0.0)
Imports: stats, graphics, grDevices, utils, vegan, ggplot2, phangorn,
ape (>= 3.1-1), igraph, methods, ade4, pegas, reshape2, dplyr
(>= 0.4), boot, shiny, magrittr
Suggests: testthat, knitr, rmarkdown, knitcitations, polysat, poweRlaw,
cowplot
License: GPL-2 | GPL-3
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-06-08 23:19:50 UTC; zhian
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Sydney E. Everhart [ctb, dtc],
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb],
Erik Sotka [ctb],
Brian J. Knaus [ctb],
Niklaus J. Grunwald [ths]
Repository: CRAN
Date/Publication: 2016-06-13 17:17:59

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'poppr' ...
** package 'poppr' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c bitwise_distance.c -o bitwise_distance.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c mlg_clustering.c -o mlg_clustering.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c mlg_counter.c -o mlg_counter.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c msn.c -o msn.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c omp_test.c -o omp_test.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c permut_shuffler.c -o permut_shuffler.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c poppr_distance.c -o poppr_distance.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o poppr.so bitwise_distance.o mlg_clustering.o mlg_counter.o msn.o omp_test.o permut_shuffler.o poppr_distance.o -fopenmp -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/poppr/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'poppr'
    finding HTML links ... done
    Aeut                                    html  
    finding level-2 HTML links ... done

    MLG-accessors                           html  
    MLG-class                               html  
    MLG-method                              html  
    Pinf                                    html  
    Pram                                    html  
    aboot                                   html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/aboot.Rd:57: missing file link 'phylo'
    bitwise.dist                            html  
    bitwise.ia                              html  
    bootgen-class                           html  
    bootgen-methods                         html  
    bruvo.boot                              html  
    bruvo.dist                              html  
    bruvo.msn                               html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/bruvo.msn.Rd:101: missing file link 'minimum.spanning.tree'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/bruvo.msn.Rd:178: missing file link 'minimum.spanning.tree'
    bruvomat-class                          html  
    bruvomat-methods                        html  
    clonecorrect                            html  
    coercion-methods                        html  
    cutoff_predictor                        html  
    diss.dist                               html  
    diversity_boot                          html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/diversity_boot.Rd:12: missing file link 'mlg.table'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/diversity_boot.Rd:97: missing file link 'rmultinom'
    diversity_ci                            html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/diversity_ci.Rd:14: missing file link 'mlg.table'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/diversity_ci.Rd:26: missing file link 'mlg.table'
    diversity_stats                         html  
    filter_stats                            html  
    fix_replen                              html  
    genclone-class                          html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/genclone-class.Rd:68: missing file link 'strata'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/genclone-class.Rd:68: missing file link 'setPop'
    genclone-method                         html  
    genetic_distance                        html  
    genind2genalex                          html  
    genotype_curve                          html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/genotype_curve.Rd:12: missing file link 'loci'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/genotype_curve.Rd:42: missing file link 'loci'
    getfile                                 html  
    grapes-greater-than-grapes              html  
    greycurve                               html  
    ia                                      html  
    imsn                                    html  
    incomp                                  html  
    info_table                              html  
    informloci                              html  
    is.clone                                html  
    levels-methods                          html  
    locus_table                             html  
    missingno                               html  
    mlg                                     html  
    mlg.filter                              html  
    mll-method                              html  
    mll.custom                              html  
    mll.reset-method                        html  
    monpop                                  html  
    old2new_genclone                        html  
    partial_clone                           html  
    pgen                                    html  
    plot_filter_stats                       html  
    plot_poppr_msn                          html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/plot_poppr_msn.Rd:76: missing file link 'layout.auto'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/plot_poppr_msn.Rd:247: missing file link 'layout.auto'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/plot_poppr_msn.Rd:249: missing file link 'delete.edges'
    poppr-package                           html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/poppr-package.Rd:18: missing file link 'adegenet'
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/poppr-package.Rd:60: missing file link 'adegenet'
    poppr                                   html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/poppr.Rd:21: missing file link 'popNames'
    poppr.all                               html  
    poppr.amova                             html  
    poppr.msn                               html  
    poppr_has_parallel                      html  
    popsub                                  html  
    private_alleles                         html  
Rd warning: /tmp/RtmpTFNRyO/R.INSTALL747c5e6ef908/poppr/man/private_alleles.Rd:46: missing file link 'strata'
    psex                                    html  
    rare_allele_correction                  html  
    read.genalex                            html  
    recode_polyploids                       html  
    rraf                                    html  
    rrmlg                                   html  
    samp.ia                                 html  
    shufflepop                              html  
    snpclone-coercion-methods               html  
    snpclone-method                         html  
    test_replen                             html  
    unique-methods                          html  
    win.ia                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (poppr)
Making 'packages.html' ... done