Last data update: 2014.03.03


Package: LEA
Title: LEA: an R package for Landscape and Ecological Association
Version: 1.4.0
Date: 2016-04-03
Author: Eric Frichot <>, Olivier Francois
Maintainer: Eric Frichot <>
Depends: R (>= 3.0.2), methods, stats, utils
Description: LEA is an R package dedicated to landscape genomics and
ecological association tests. LEA can run analyses of
population structure and genome scans for local adaptation. It
includes statistical methods for estimating ancestry
coefficients from large genotypic matrices and evaluating the
number of ancestral populations (snmf, pca); and identifying
genetic polymorphisms that exhibit high correlation with some
environmental gradient or with the variables used as proxies
for ecological pressures (lfmm), and controlling the false
discovery rate. LEA is mainly based on optimized C programs
that can scale with the dimension of very large data sets.
License: GPL-3
biocViews: Software, StatisticalMethod, Clustering, Regression
NeedsCompilation: yes
Packaged: 2016-05-04 06:10:10 UTC; biocbuild

● BiocViews: Clustering, Regression, Software, StatisticalMethod
5 images, 37 functions, 0 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'LEA' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_LFMM.c -o R_LFMM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_crossEntropy.c -o R_crossEntropy.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_createDataSet.c -o R_createDataSet.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_sNMF.c -o R_sNMF.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_ancestrymap2geno.c -o R_ancestrymap2geno.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_ancestrymap2lfmm.c -o R_ancestrymap2lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_geno2lfmm.c -o R_geno2lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_lfmm2geno.c -o R_lfmm2geno.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_pca.c -o R_pca.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_ped2geno.c -o R_ped2geno.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_ped2lfmm.c -o R_ped2lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_vcf2geno.c -o R_vcf2geno.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_tracyWidom.c -o R_tracyWidom.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c R_init_LEA.c -o R_init_LEA.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c bituint/bituint.c -o bituint/bituint.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c bituint/calc_bituint.c -o bituint/calc_bituint.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c bituint/io_geno_bituint.c -o bituint/io_geno_bituint.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c bituint/slice_bituint.c -o bituint/slice_bituint.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c bituint/thread_bituint.c -o bituint/thread_bituint.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c convert/ancestrymap.c -o convert/ancestrymap.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c convert/geno.c -o convert/geno.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c convert/ped.c -o convert/ped.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c convert/vcf2geno.c -o convert/vcf2geno.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c convert/geno2lfmm.c -o convert/geno2lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c convert/lfmm2geno.c -o convert/lfmm2geno.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c convert/register_convert.c -o convert/register_convert.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c createDataSet/createDataSet.c -o createDataSet/createDataSet.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c createDataSet/error_cds.c -o createDataSet/error_cds.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c createDataSet/print_cds.c -o createDataSet/print_cds.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c createDataSet/register_cds.c -o createDataSet/register_cds.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c crossEntropy/crossEntropy.c -o crossEntropy/crossEntropy.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c crossEntropy/error_ce.c -o crossEntropy/error_ce.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c crossEntropy/print_ce.c -o crossEntropy/print_ce.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c crossEntropy/register_ce.c -o crossEntropy/register_ce.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c io/io_data_double.c -o io/io_data_double.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c io/io_data_float.c -o io/io_data_float.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c io/io_data_int.c -o io/io_data_int.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c io/io_error.c -o io/io_error.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c io/io_tools.c -o io/io_tools.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c io/print_bar.c -o io/print_bar.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/beta.c -o LFMM/beta.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/error_lfmm.c -o LFMM/error_lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/lfmm_k0.c -o LFMM/lfmm_k0.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/slice_lfmm.c -o LFMM/slice_lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/U.c -o LFMM/U.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/beta_k0.c -o LFMM/beta_k0.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/lfmm_algo.c -o LFMM/lfmm_algo.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/print_lfmm.c -o LFMM/print_lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/thread_lfmm.c -o LFMM/thread_lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/V.c -o LFMM/V.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/data_lfmm.c -o LFMM/data_lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/LFMM.c -o LFMM/LFMM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/register_lfmm.c -o LFMM/register_lfmm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c LFMM/thread_var.c -o LFMM/thread_var.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/cholesky.c -o matrix/cholesky.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/error_matrix.c -o matrix/error_matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/normalize.c -o matrix/normalize.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/slice_matrix.c -o matrix/slice_matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/data.c -o matrix/data.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/inverse.c -o matrix/inverse.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/rand.c -o matrix/rand.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/sylvester.c -o matrix/sylvester.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/diagonalize.c -o matrix/diagonalize.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/matrix.c -o matrix/matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/random_projection.c -o matrix/random_projection.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c matrix/thread_matrix.c -o matrix/thread_matrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c nnlsm/blockpivot.c -o nnlsm/blockpivot.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c nnlsm/nnlsm.c -o nnlsm/nnlsm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c nnlsm/solvenormaleqcomb.c -o nnlsm/solvenormaleqcomb.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c nnlsm/sort.c -o nnlsm/sort.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c pca/calc_cov.c -o pca/calc_cov.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c pca/error_pca.c -o pca/error_pca.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c pca/pca.c -o pca/pca.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c pca/print_pca.c -o pca/print_pca.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c pca/register_pca.c -o pca/register_pca.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/als.c -o sNMF/als.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/als_k1.c -o sNMF/als_k1.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/criteria.c -o sNMF/criteria.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/print_snmf.c -o sNMF/print_snmf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/sNMF.c -o sNMF/sNMF.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/thread_Q.c -o sNMF/thread_Q.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/als_F.c -o sNMF/als_F.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/als_Q.c -o sNMF/als_Q.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/error_snmf.c -o sNMF/error_snmf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/register_snmf.c -o sNMF/register_snmf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/thread_F.c -o sNMF/thread_F.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c sNMF/thread_snmf.c -o sNMF/thread_snmf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/beta_distribution.c -o stats/beta_distribution.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/gamma_density.c -o stats/gamma_density.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/ln_beta_function.c -o stats/ln_beta_function.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/beta_function.c -o stats/beta_function.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/gamma_distribution.c -o stats/gamma_distribution.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/ln_gamma_function.c -o stats/ln_gamma_function.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/entire_incomplete_gamma_function.c -o stats/entire_incomplete_gamma_function.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/gamma_dist_tables.c -o stats/gamma_dist_tables.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/student_t_distribution.c -o stats/student_t_distribution.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/factorial.c -o stats/factorial.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c stats/gamma_function.c -o stats/gamma_function.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c tracyWidom/error_tracyWidom.c -o tracyWidom/error_tracyWidom.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c tracyWidom/register_tracyWidom.c -o tracyWidom/register_tracyWidom.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c tracyWidom/print_tracyWidom.c -o tracyWidom/print_tracyWidom.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I. -I/usr/local/include    -fpic  -g -O2  -c tracyWidom/tracyWidom.c -o tracyWidom/tracyWidom.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o R_LFMM.o R_crossEntropy.o R_createDataSet.o R_sNMF.o R_ancestrymap2geno.o R_ancestrymap2lfmm.o R_geno2lfmm.o R_lfmm2geno.o R_pca.o R_ped2geno.o R_ped2lfmm.o R_vcf2geno.o R_tracyWidom.o R_init_LEA.o bituint/bituint.o bituint/calc_bituint.o bituint/io_geno_bituint.o bituint/slice_bituint.o bituint/thread_bituint.o convert/ancestrymap.o convert/geno.o convert/ped.o convert/vcf2geno.o convert/geno2lfmm.o convert/lfmm2geno.o convert/register_convert.o createDataSet/createDataSet.o createDataSet/error_cds.o createDataSet/print_cds.o createDataSet/register_cds.o crossEntropy/crossEntropy.o crossEntropy/error_ce.o crossEntropy/print_ce.o crossEntropy/register_ce.o io/io_data_double.o io/io_data_float.o io/io_data_int.o io/io_error.o io/io_tools.o io/print_bar.o LFMM/beta.o LFMM/error_lfmm.o LFMM/lfmm_k0.o LFMM/slice_lfmm.o LFMM/U.o LFMM/beta_k0.o LFMM/lfmm_algo.o LFMM/print_lfmm.o LFMM/thread_lfmm.o LFMM/V.o LFMM/data_lfmm.o LFMM/LFMM.o LFMM/register_lfmm.o LFMM/thread_var.o matrix/cholesky.o matrix/error_matrix.o matrix/normalize.o matrix/slice_matrix.o matrix/data.o matrix/inverse.o matrix/rand.o matrix/sylvester.o matrix/diagonalize.o matrix/matrix.o matrix/random_projection.o matrix/thread_matrix.o nnlsm/blockpivot.o nnlsm/nnlsm.o nnlsm/solvenormaleqcomb.o nnlsm/sort.o pca/calc_cov.o pca/error_pca.o pca/pca.o pca/print_pca.o pca/register_pca.o sNMF/als.o sNMF/als_k1.o sNMF/criteria.o sNMF/print_snmf.o sNMF/sNMF.o sNMF/thread_Q.o sNMF/als_F.o sNMF/als_Q.o sNMF/error_snmf.o sNMF/register_snmf.o sNMF/thread_F.o sNMF/thread_snmf.o stats/beta_distribution.o stats/gamma_density.o stats/ln_beta_function.o stats/beta_function.o stats/gamma_distribution.o stats/ln_gamma_function.o stats/entire_incomplete_gamma_function.o stats/gamma_dist_tables.o stats/student_t_distribution.o stats/factorial.o stats/gamma_function.o tracyWidom/error_tracyWidom.o tracyWidom/register_tracyWidom.o tracyWidom/print_tracyWidom.o tracyWidom/tracyWidom.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/LEA/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'LEA'
** help
*** installing help indices
  converting help for package 'LEA'
    finding HTML links ... done
    G                                       html  
    Q                                       html  
    Replop-package                          html  
    adjusted_pvalues                        html  
    ancestrymap                             html  
    ancestrymap2geno                        html  
    ancestrymap2lfmm                        html  
    crossEntropy                            html  
    env                                     html  
    geno                                    html  
    geno2lfmm                               html  
    lfmm                                    html  
    lfmm2geno                               html  
    main_LFMM                               html  
    main_createDataSet                      html  
    main_crossEntropyEstimation             html  
    main_pca                                html  
    main_sNMF                               html  
    main_tracyWidom                         html  
    mlog10pvalues                           html  
    ped                                     html  
    ped2geno                                html  
    ped2lfmm                                html  
    pvalues                                 html  
    readEnv                                 html  
    readGeno                                html  
    readLfmm                                html  
    readZscore                              html  
    tutorial                                html  
    vcf                                     html  
    vcf2geno                                html  
    vcf2lfmm                                html  
    writeEnv                                html  
    writeGeno                               html  
    writeLFMM                               html  
    zscore                                  html  
    zscores                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Making 'packages.html' ... done