gaston

Package: gaston
Type: Package
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Version: 1.4.5
Date: 2016-03-30
Encoding: UTF-8
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
License: GPL-3
LinkingTo: Rcpp,RcppParallel,RcppEigen
Depends: Rcpp, RcppParallel, methods, WhopGenome, LDheatmap
NeedsCompilation: yes
LazyLoad: yes
LazyData: yes
Packaged: 2016-03-30 14:20:54 UTC; rv
Repository: CRAN
Date/Publication: 2016-03-30 20:35:14

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'gaston' ...
** package 'gaston' 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" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c diago_wrapers.cpp -o diago_wrapers.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c export-aireml-1k.cpp -o export-aireml-1k.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c export-aireml-nk.cpp -o export-aireml-nk.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c gwas_lmm_diago_lrt.cpp -o gwas_lmm_diago_lrt.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c gwas_lmm_diago_lrt_mt.cpp -o gwas_lmm_diago_lrt_mt.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c gwas_lmm_diago_wald.cpp -o gwas_lmm_diago_wald.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c gwas_lmm_diago_wald_mt.cpp -o gwas_lmm_diago_wald_mt.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c hwe.cpp -o hwe.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c hwe_chi.cpp -o hwe_chi.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c isnullptr.cpp -o isnullptr.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c lmm_diago.cpp -o lmm_diago.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c lmm_diago_full.cpp -o lmm_diago_full.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c lmm_diago_nocovar.cpp -o lmm_diago_nocovar.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c loubar.cpp -o loubar.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_bed.cpp -o m4_bed.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_bind_inds.cpp -o m4_bind_inds.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_bind_snps.cpp -o m4_bind_snps.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_conversion.cpp -o m4_conversion.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_dims.cpp -o m4_dims.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_exports.cpp -o m4_exports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_extractind.cpp -o m4_extractind.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_extractsnp.cpp -o m4_extractsnp.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_kinship.cpp -o m4_kinship.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_kinship_p.cpp -o m4_kinship_p.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_ld.cpp -o m4_ld.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_ldp.cpp -o m4_ldp.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_ldthin_left.cpp -o m4_ldthin_left.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_ldthin_random.cpp -o m4_ldthin_random.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_ldthin_right.cpp -o m4_ldthin_right.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_prod2_ms.cpp -o m4_prod2_ms.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_prod2_p.cpp -o m4_prod2_p.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_prod_ms.cpp -o m4_prod_ms.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_prod_p.cpp -o m4_prod_p.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_read_vcf.cpp -o m4_read_vcf.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_stats.cpp -o m4_stats.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c m4_transpose.cpp -o m4_transpose.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c matrix-varia.cpp -o matrix-varia.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c matrix4.cpp -o matrix4.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppParallel/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c optimize.cpp -o optimize.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o gaston.so diago_wrapers.o export-aireml-1k.o export-aireml-nk.o gwas_lmm_diago_lrt.o gwas_lmm_diago_lrt_mt.o gwas_lmm_diago_wald.o gwas_lmm_diago_wald_mt.o hwe.o hwe_chi.o isnullptr.o lmm_diago.o lmm_diago_full.o lmm_diago_nocovar.o loubar.o m4_bed.o m4_bind_inds.o m4_bind_snps.o m4_conversion.o m4_dims.o m4_exports.o m4_extractind.o m4_extractsnp.o m4_kinship.o m4_kinship_p.o m4_ld.o m4_ldp.o m4_ldthin_left.o m4_ldthin_random.o m4_ldthin_right.o m4_prod2_ms.o m4_prod2_p.o m4_prod_ms.o m4_prod_p.o m4_read_vcf.o m4_stats.o m4_transpose.o matrix-varia.o matrix4.o optimize.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/gaston/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppParallel::LdFlags' when loading 'gaston'
Creating a new generic function for 'cbind' in package 'gaston'
Creating a new generic function for 'rbind' in package 'gaston'
** help
*** installing help indices
  converting help for package 'gaston'
    finding HTML links ... done
    AGT                                     html  
    GRM                                     html  
    LCT                                     html  
    LD                                      html  
    LD.thin                                 html  
    TTN                                     html  
    as.bed.matrix                           html  
    association.test                        html  
    bed.loadings                            html  
    bed.matrix-class                        html  
    gaston-package                          html  
Rd warning: /tmp/Rtmpyw1ovR/R.INSTALL7c7d73039850/gaston/man/gaston-package.Rd:39: missing file link 'WhopGenome-package'
    lik.contour                             html  
    lmm.aireml                              html  
    lmm.diago                               html  
    lmm.diago.likelihood                    html  
    lmm.simu                                html  
    random.pm                               html  
    read.bed.matrix                         html  
    read.vcf                                html  
Rd warning: /tmp/Rtmpyw1ovR/R.INSTALL7c7d73039850/gaston/man/read.vcf.Rd:16: missing file link 'WhopGenome-package'
    reshape.GRM                             html  
    select.inds                             html  
    select.snps                             html  
    set.genomic.sex                         html  
    set.hwe                                 html  
    set.stats                               html  
    write.bed.matrix                        html  
Rd warning: /tmp/Rtmpyw1ovR/R.INSTALL7c7d73039850/gaston/man/write.bed.matrix.Rd:37: missing file link 'saveRDS'
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppParallel::LdFlags' when loading 'gaston'
* DONE (gaston)
Making 'packages.html' ... done