pegas

Package: pegas
Version: 0.9
Date: 2016-04-14
Title: Population and Evolutionary Genetics Analysis System
Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr"),
person("Thibaut", "Jombart", role = c("aut", "cph")),
person("Klaus", "Schliep", role = c("aut", "cph")),
person("Alastair", "Potts", role = c("aut", "cph")),
person("David", "Winter", role = c("aut", "cph")))
Depends: R (>= 2.6.0), ape (>= 2.4), adegenet
Imports: graphics, utils
ZipData: no
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
License: GPL (>= 2)
URL: http://ape-package.ird.fr/pegas.html
NeedsCompilation: yes
Packaged: 2016-04-14 09:48:45 UTC; paradis
Author: Emmanuel Paradis [aut, cre, cph],
Thibaut Jombart [aut, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Repository: CRAN
Date/Publication: 2016-04-16 00:03:13

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'pegas' ...
** package 'pegas' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pegas.c -o pegas.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readVCFbin.c -o readVCFbin.o
readVCFbin.c: In function 'read_bin_pegas':
readVCFbin.c:32:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread(p, 1, sz, fl);
     ^
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o pegas.so pegas.o readVCFbin.o -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/pegas/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'pegas'
    finding HTML links ... done
    Fst                                     html  
    LD                                      html  
    LDscan                                  html  
    MMD                                     html  
    R2.test                                 html  
    VCFloci                                 html  
    alleles2loci                            html  
    amova                                   html  
    bind.loci                               html  
    conversion                              html  
    diffHaplo                               html  
    edit.loci                               html  
    geoTrans                                html  
    geod                                    html  
    haploFreq                               html  
    haploNet                                html  
    haplotype                               html  
    haplotype.loci                          html  
    heterozygosity                          html  
    hw.test                                 html  
    finding level-2 HTML links ... done

    jaguar                                  html  
    mst                                     html  
    na.omit.loci                            html  
Rd warning: /tmp/RtmpW0GnsW/R.INSTALL53d2534837ed/pegas/man/na.omit.loci.Rd:5: missing file link 'na.omit'
    nuc.div                                 html  
Rd warning: /tmp/RtmpW0GnsW/R.INSTALL53d2534837ed/pegas/man/nuc.div.Rd:48: missing file link 'GC.content'
    pegas-package                           html  
    read.gtx                                html  
    read.loci                               html  
    read.vcf                                html  
    replot                                  html  
    rr.test                                 html  
    site.spectrum                           html  
    subset.haplotype                        html  
    summary.loci                            html  
    tajima.test                             html  
    theta.h                                 html  
    theta.k                                 html  
    theta.msat                              html  
    theta.s                                 html  
    theta.tree                              html  
    utilities                               html  
    write.loci                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pegas)
Making 'packages.html' ... done