PopGenome

Package: PopGenome
Type: Package
Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Version: 2.1.6
Date: 2015-05-1
Author: Bastian Pfeifer [aut, cre], Ulrich Wittelsbuerger [ctb], Heng Li [ctb], Bob Handsaker [ctb]
Authors@R: c( person("Bastian", "Pfeifer", role = c("aut", "cre"), email = "Bastian.Pfeifer@uni-duesseldorf.de"),
person("Ulrich", "Wittelsbuerger", role = "ctb"),
person("Heng", "Li", role = "ctb"),
person("Bob", "Handsaker", role = "ctb") )
Maintainer: Bastian Pfeifer <Bastian.Pfeifer@uni-duesseldorf.de>
Depends: R (>= 2.14.2), ff
Imports: methods
Suggests: parallel, bigmemory, BASIX, WhopGenome
Description: Provides efficient tools for population genomics data analysis,
able to process individual loci, large sets of loci, or whole genomes. PopGenome not only
implements a wide range of population genetics statistics, but also facilitates the easy
implementation of new algorithms by other researchers. PopGenome is optimized for speed via
the seamless integration of C code.
License: GPL-3
URL: http://popgenome.weebly.com
LazyLoad: yes
Copyright: inst/COPYRIGHTS
SystemRequirements: zlib headers and library.
Repository: CRAN
NeedsCompilation: yes
Packaged: 2015-05-02 13:33:06 UTC; user
Date/Publication: 2015-05-04 23:40:49

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'PopGenome' ...
** package 'PopGenome' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/readdnapp.cpp -o whopgenome/readdnapp.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_codemat.cpp -o whopgenome/whopgen_codemat.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_filtering.cpp -o whopgenome/whopgen_filtering.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_main.cpp -o whopgenome/whopgen_main.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_read.cpp -o whopgenome/whopgen_read.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_region.cpp -o whopgenome/whopgen_region.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_rsupport.cpp -o whopgenome/whopgen_rsupport.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_samples.cpp -o whopgenome/whopgen_samples.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_tools.cpp -o whopgenome/whopgen_tools.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whopgen_vcf.cpp -o whopgenome/whopgen_vcf.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whop_r_dataframe.cpp -o whopgenome/whop_r_dataframe.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whoptbi_info.cpp -o whopgenome/whoptbi_info.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whoptbi_read.cpp -o whopgenome/whoptbi_read.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whoptbi_region.cpp -o whopgenome/whoptbi_region.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whoptbi_Rifc.cpp -o whopgenome/whoptbi_Rifc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c whopgenome/whoptbi_main.cpp -o whopgenome/whoptbi_main.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c VCF_split.cpp -o VCF_split.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ap_pop_ancestral_C.c -o ap_pop_ancestral_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ap_pop_C.c -o ap_pop_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c C_get_sfreqh_C.c -o C_get_sfreqh_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c code_nucs.c -o code_nucs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c combnsum2_C.c -o combnsum2_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c combnsum_C.c -o combnsum_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c CompareVEK.c -o CompareVEK.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c compute_FREQ_C.c -o compute_FREQ_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c compute_FREQOUT_C.c -o compute_FREQOUT_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c find_lines.c -o find_lines.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c find_windowC.c -o find_windowC.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fittingGFFC++.c -o fittingGFFC++.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c get_dim_fasta.c -o get_dim_fasta.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c get_gff_info_C.c -o get_gff_info_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c get_ind_fasta.c -o get_ind_fasta.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c get_segsites_C.c -o get_segsites_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c makeBial.c -o makeBial.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c makeBialMatrix.c -o makeBialMatrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c my_match_C.c -o my_match_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c my_unique_C.c -o my_unique_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R2_C.c -o R2_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c verify_ancestral_C.c -o verify_ancestral_C.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c filldiplomatrix.c -o filldiplomatrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c myReadVCFC.c -o myReadVCFC.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c tabix/bedidx.c -o tabix/bedidx.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c tabix/bgzf.c -o tabix/bgzf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c tabix/index.c -o tabix/index.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c tabix/knetfile.c -o tabix/knetfile.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c tabix/kstring.c -o tabix/kstring.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o PopGenome.so whopgenome/readdnapp.o whopgenome/whopgen_codemat.o whopgenome/whopgen_filtering.o whopgenome/whopgen_main.o whopgenome/whopgen_read.o whopgenome/whopgen_region.o whopgenome/whopgen_rsupport.o whopgenome/whopgen_samples.o whopgenome/whopgen_tools.o whopgenome/whopgen_vcf.o whopgenome/whop_r_dataframe.o whopgenome/whoptbi_info.o whopgenome/whoptbi_read.o whopgenome/whoptbi_region.o whopgenome/whoptbi_Rifc.o whopgenome/whoptbi_main.o VCF_split.o ap_pop_ancestral_C.o ap_pop_C.o C_get_sfreqh_C.o code_nucs.o combnsum2_C.o combnsum_C.o CompareVEK.o compute_FREQ_C.o compute_FREQOUT_C.o find_lines.o find_windowC.o fittingGFFC++.o get_dim_fasta.o get_gff_info_C.o get_ind_fasta.o get_segsites_C.o makeBial.o makeBialMatrix.o my_match_C.o my_unique_C.o R2_C.o verify_ancestral_C.o filldiplomatrix.o myReadVCFC.o tabix/bedidx.o tabix/bgzf.o tabix/index.o tabix/knetfile.o tabix/kstring.o -lz -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/PopGenome/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'PopGenome'
    finding HTML links ... done
    Achaz.stats                             html  
    BayeScanR                               html  
    F_ST.stats-methods                      html  
    F_ST.stats.2-methods                    html  
    GENOME-class                            html  
    GFF_split_into_scaffolds                html  
    MKT-methods                             html  
    MS                                      html  
    MS_getStats                             html  
    PG_plot.biallelic.matrix                html  
    PopGenome                               html  
    PopGplot                                html  
    VCF_split_into_scaffolds                html  
    Whop_readVCF                            html  
    calc.R2-methods                         html  
    codontable                              html  
    concatenate.classes                     html  
    concatenate.regions                     html  
    count.unknowns-methods                  html  
    create.PopGenome.method                 html  
    detail.stats-methods                    html  
    diversity.stats-methods                 html  
    fasta_file                              html  
    get.biallelic.matrix-methods            html  
    get.codons-methods                      html  
    get.feature.names                       html  
    get.individuals-methods                 html  
    get.status-methods                      html  
    getBayes-methods                        html  
    get_gff_info                            html  
    gff_file                                html  
    introgression.stats                     html  
    jack.knife.transform-methods            html  
    linkage.stats-methods                   html  
    load.session                            html  
    mult.linkage.stats                      html  
    neutrality.stats-methods                html  
    read.big.fasta                          html  
    readData                                html  
    readHapMap                              html  
    readMS                                  html  
    readSNP                                 html  
    readVCF                                 html  
    recomb.stats-methods                    html  
    region.as.fasta                         html  
    save.session                            html  
    set.outgroup-methods                    html  
    set.populations-methods                 html  
    set.ref.positions                       html  
    set.synnonsyn-methods                   html  
    show.slots-methods                      html  
    sliding.window.transform-methods        html  
    snp_file                                html  
    split_data_into_GFF_attributes          html  
    splitting.data-methods                  html  
    sweeps.stats-methods                    html  
    test.params-class                       html  
    vcf_file                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PopGenome)
Making 'packages.html' ... done