SNPRelate

Package: SNPRelate
Type: Package
Title: Parallel Computing Toolset for Relatedness and Principal
Component Analysis of SNP Data
Version: 1.6.4
Date: 2016-06-14
Depends: R (>= 2.15), gdsfmt (>= 1.8.3)
LinkingTo: gdsfmt
Suggests: parallel, RUnit, knitr, MASS, BiocGenerics
Enhances: SeqArray (>= 1.11.12)
Authors@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre", "cph"),
email="zhengx@u.washington.edu"),
person("Stephanie", "Gogarten", role="ctb"),
person("Cathy", "Laurie", role="ctb"),
person("Bruce", "Weir", role=c("ctb", "ths"),
email="bsweir@u.washington.edu"))
Description: Genome-wide association studies (GWAS) are widely used to
investigate the genetic basis of diseases and traits, but they
pose many computational challenges. We developed an R package
SNPRelate to provide a binary format for single-nucleotide
polymorphism (SNP) data in GWAS utilizing CoreArray Genomic
Data Structure (GDS) data files. The GDS format offers the
efficient operations specifically designed for integers with
two bits, since a SNP could occupy only two bits. SNPRelate is
also designed to accelerate two key computations on SNP data
using parallel computing for multi-core symmetric
multiprocessing computer architectures: Principal Component
Analysis (PCA) and relatedness analysis using
Identity-By-Descent measures. The SNP GDS format is also used by the
GWASTools package with the support of S4 classes and generic functions.
The extended GDS format is implemented in the SeqArray package to
support the storage of single nucleotide variations (SNVs),
insertion/deletion polymorphism (indel) and structural variation calls.
License: GPL-3
VignetteBuilder: knitr
URL: http://github.com/zhengxwen/SNPRelate
http://corearray.sourceforge.net/tutorials/SNPRelate/
BugReports: http://github.com/zhengxwen/SNPRelate/issues
biocViews: Infrastructure, Genetics, StatisticalMethod,
PrincipalComponent
NeedsCompilation: yes
Packaged: 2016-06-15 04:42:52 UTC; biocbuild
Author: Xiuwen Zheng [aut, cre, cph],
Stephanie Gogarten [ctb],
Cathy Laurie [ctb],
Bruce Weir [ctb, ths]
Maintainer: Xiuwen Zheng <zhengx@u.washington.edu>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SNPRelate' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c R_SNPRelate.c -o R_SNPRelate.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c SNPRelate.cpp -o SNPRelate.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c ThreadPool.cpp -o ThreadPool.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c dGenGWAS.cpp -o dGenGWAS.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c dVect.cpp -o dVect.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genFst.cpp -o genFst.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genHWE.cpp -o genHWE.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genIBD.cpp -o genIBD.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genIBS.cpp -o genIBS.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genKING.cpp -o genKING.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genLD.cpp -o genLD.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genPCA.cpp -o genPCA.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genRec.cpp -o genRec.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/gdsfmt/include"   -fpic  -g -O2  -c genSlideWin.cpp -o genSlideWin.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genRec.o genSlideWin.o -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lRblas -L/home/ddbj/local/lib64/R/lib -lRlapack -lpthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/SNPRelate/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SNPRelate'
    finding HTML links ... done
    SNPGDSFileClass-class                   html  
    SNPRelate-package                       html  
    hapmap_geno                             html  
    snpgdsAdmixProp                         html  
    snpgdsAlleleSwitch                      html  
    snpgdsApartSelection                    html  
    snpgdsBED2GDS                           html  
    finding level-2 HTML links ... done

    snpgdsClose                             html  
    snpgdsCombineGeno                       html  
    snpgdsCreateGeno                        html  
    snpgdsCreateGenoSet                     html  
    snpgdsCutTree                           html  
    snpgdsDiss                              html  
    snpgdsDrawTree                          html  
    snpgdsEIGMIX                            html  
    snpgdsErrMsg                            html  
    snpgdsExampleFileName                   html  
    snpgdsFst                               html  
    snpgdsGDS2BED                           html  
    snpgdsGDS2Eigen                         html  
    snpgdsGDS2PED                           html  
    snpgdsGEN2GDS                           html  
    snpgdsGRM                               html  
    snpgdsGetGeno                           html  
    snpgdsHCluster                          html  
    snpgdsHWE                               html  
    snpgdsIBDKING                           html  
    snpgdsIBDMLE                            html  
    snpgdsIBDMLELogLik                      html  
    snpgdsIBDMoM                            html  
    snpgdsIBDSelection                      html  
    snpgdsIBS                               html  
    snpgdsIBSNum                            html  
    snpgdsIndInb                            html  
    snpgdsIndInbCoef                        html  
    snpgdsLDMat                             html  
    snpgdsLDpair                            html  
    snpgdsLDpruning                         html  
    snpgdsOpen                              html  
    snpgdsOption                            html  
    snpgdsPCA                               html  
    snpgdsPCACorr                           html  
    snpgdsPCASNPLoading                     html  
    snpgdsPCASampLoading                    html  
    snpgdsPED2GDS                           html  
    snpgdsPairIBD                           html  
    snpgdsPairIBDMLELogLik                  html  
    snpgdsPairScore                         html  
    snpgdsSNPList                           html  
    snpgdsSNPListClass                      html  
    snpgdsSNPListIntersect                  html  
    snpgdsSNPListStrand                     html  
    snpgdsSNPRateFreq                       html  
    snpgdsSampMissRate                      html  
    snpgdsSelectSNP                         html  
    snpgdsSlidingWindow                     html  
    snpgdsSummary                           html  
    snpgdsTranspose                         html  
    snpgdsVCF2GDS                           html  
    snpgdsVCF2GDS_R                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPRelate)
Making 'packages.html' ... done