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Last data update: 2014.03.03

snpStats

Package: snpStats
Title: SnpMatrix and XSnpMatrix classes and methods
Version: 1.22.0
Date: 2015-12-19
Author: David Clayton <dc208@cam.ac.uk>
Description: Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
Maintainer: David Clayton <dc208@cam.ac.uk>
Depends: R (>= 2.10.0), survival, Matrix, methods
Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
Suggests: hexbin
License: GPL-3
Collate: ss.R contingency.table.R convert.R compare.R glm-test.R
imputation.R indata.R long.R misc.R ld.R mvtests.R pedfile.R
outdata.R plink.R qc.R qq-chisq.R single.R tdt-single.R
structure.R xstuff.R
LazyLoad: yes
biocViews: Microarray, SNP, GeneticVariability
Packaged: 2016-05-04 03:07:49 UTC; biocbuild
NeedsCompilation: yes

● BiocViews: GeneticVariability, Microarray, SNP
● 2 images, 49 functions, 6 datasets
● Reverse Depends: 5

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'snpStats' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Runcertain.c -o Runcertain.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bind.c -o bind.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c count_gt.c -o count_gt.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c covwin.c -o covwin.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c force_hom.c -o force_hom.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c fst.c -o fst.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c glm_test.c -o glm_test.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c glm_test_R.c -o glm_test_R.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hash_index.c -o hash_index.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hphase.c -o hphase.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c imputation.c -o imputation.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c in.c -o in.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c input.c -o input.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c invert.c -o invert.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ipf.c -o ipf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ld.c -o ld.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c misc.c -o misc.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mla.c -o mla.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c mvphenotype.c -o mvphenotype.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c outdata.c -o outdata.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c plink.c -o plink.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c read_uncertain.c -o read_uncertain.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readped.c -o readped.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c single_snp_tests.c -o single_snp_tests.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c snp_summary.c -o snp_summary.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c snpmpy.c -o snpmpy.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c solve_cubic.c -o solve_cubic.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c structure.c -o structure.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c subset.c -o subset.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c switch.c -o switch.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c tdt.c -o tdt.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c testBig.c -o testBig.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c uncertain.c -o uncertain.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o snpStats.so Runcertain.o bind.o count_gt.o covwin.o force_hom.o fst.o glm_test.o glm_test_R.o hash_index.o hphase.o imputation.o in.o input.o invert.o ipf.o ld.o misc.o mla.o mvphenotype.o outdata.o plink.o read_uncertain.o readped.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o structure.o subset.o switch.o tdt.o testBig.o uncertain.o -lz -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/snpStats/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'snpStats'
** help
*** installing help indices
  converting help for package 'snpStats'
    finding HTML links ... done
    Fst                                     html  
    GlmEstimates-class                      html  
    GlmTests-class                          html  
    ImputationRules-class                   html  
    SingleSnpTests-class                    html  
    SnpMatrix-class                         html  
    XSnpMatrix-class                        html  
    chi.squared                             html  
    convert.snpMatrix                       html  
    example-new                             html  
    families                                html  
    filter.rules                            html  
    for.exercise                            html  
    glm.test.control                        html  
    ibsCount                                html  
    ibsDist                                 html  
    imputation.maf                          html  
    impute.snps                             html  
    ld                                      html  
    ld.example                              html  
    mean2g                                  html  
    misinherits                             html  
    mvtests                                 html  
    plotUncertainty                         html  
    pool                                    html  
    pool2                                   html  
    pp                                      html  
    qq.chisq                                html  
    random.snps                             html  
    read.beagle                             html  
    read.impute                             html  
    read.long                               html  
    read.mach                               html  
    read.pedfile                            html  
    read.plink                              html  
    read.snps.long                          html  
    row.summary                             html  
    sample                                  html  
    single.snp.tests                        html  
    sm.compare                              html  
    snp.cor                                 html  
    snp.imputation                          html  
    snp.lhs.estimates                       html  
    snp.lhs.tests                           html  
    snp.pre.multiply                        html  
    snp.rhs.estimates                       html  
    snp.rhs.tests                           html  
    snpStats-package                        html  
    switch.alleles                          html  
    tdt.snp                                 html  
    test.allele.switch                      html  
    testdata                                html  
    write.plink                             html  
    write.snp.matrix                        html  
    xxt                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (snpStats)
Making 'packages.html' ... done