R Graphical Manual

Browse All

Last data update: 2014.03.03

chopsticks

Package: chopsticks
Title: The snp.matrix and X.snp.matrix classes
Version: 1.36.0
Date: 2015-01-19
Author: Hin-Tak Leung <htl10@users.sourceforge.net>
Description: Implements classes and methods for large-scale SNP association studies
Maintainer: Hin-Tak Leung <htl10@users.sourceforge.net>
Depends: R (>= 2.10.0), survival, methods
Suggests: hexbin
License: GPL-3
URL: http://outmodedbonsai.sourceforge.net/
Collate: ld.with.R ss.R contingency.table.R glm_test.R ibs.stats.R
indata.R ld.snp.R ld.with.R.eml.R misc.R outdata.R qq_chisq.R
read.chiamo.R read.HapMap.R read.snps.pedfile.R single.R
structure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R
LazyLoad: yes
biocViews: Microarray, SNPsAndGeneticVariability, SNP,
GeneticVariability
NeedsCompilation: yes
Packaged: 2016-05-04 03:56:28 UTC; biocbuild

● BiocViews: GeneticVariability, Microarray, SNP, SNPsAndGeneticVariability
● 2 images, 35 functions, 2 datasets
● Reverse Depends: 2

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'chopsticks' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c adler32.c -o adler32.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 compress.c -o compress.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c crc32.c -o crc32.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c deflate.c -o deflate.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 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 gzio.c -o gzio.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 ibs.c -o ibs.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 infback.c -o infback.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c inffast.c -o inffast.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c inflate.c -o inflate.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c inftrees.c -o inftrees.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 inputNew.c -o inputNew.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c input_unsorted.c -o input_unsorted.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ld_graphic_eps.c -o ld_graphic_eps.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ld_with.c -o ld_with.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 outdata.c -o outdata.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pairwise_linkage.c -o pairwise_linkage.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c read_chiamo.c -o read_chiamo.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c read_hapmap.c -o read_hapmap.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c read_pedfile.c -o read_pedfile.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c read_signals.c -o read_signals.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 sdfpw.c -o sdfpw.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 solve_quadratic.c -o solve_quadratic.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 trees.c -o trees.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c uncompr.c -o uncompr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c zutil.c -o zutil.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o chopsticks.so adler32.o bind.o compress.o crc32.o deflate.o force_hom.o glm_test.o glm_test_R.o gzio.o hash_index.o ibs.o in.o infback.o inffast.o inflate.o inftrees.o input.o inputNew.o input_unsorted.o ld_graphic_eps.o ld_with.o mla.o outdata.o pairwise_linkage.o read_chiamo.o read_hapmap.o read_pedfile.o read_signals.o readped.o sdfpw.o single_snp_tests.o snp_summary.o snpmpy.o solve_cubic.o solve_quadratic.o structure.o trees.o uncompr.o zutil.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/chopsticks/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'chopsticks'
    finding HTML links ... done
    X.snp-class                             html  
    X.snp.matrix-class                      html  
    epsout.ld.snp                           html  
    for.exercise                            html  
    glm.test.control                        html  
    ibs.stats                               html  
    ibsCount                                html  
    ibsDist                                 html  
    ld.snp                                  html  
    ld.with                                 html  
    pair.result.ld.snp                      html  
    plot.snp.dprime                         html  
    qq.chisq                                html  
    read.HapMap.data                        html  
    read.pedfile.info                       html  
    read.pedfile.map                        html  
    read.snps.chiamo                        html  
    read.snps.long                          html  
    read.snps.long.old                      html  
    read.snps.pedfile                       html  
    read.wtccc.signals                      html  
    row.summary                             html  
    single.snp.tests                        html  
    snp-class                               html  
    snp.cbind                               html  
Rd warning: /tmp/RtmpIsYKOz/R.INSTALL11c23cb185cc/chopsticks/man/snp.cbind.Rd:40: missing file link 'rbind'
    snp.cor                                 html  
    snp.dprime-class                        html  
    snp.lhs.tests                           html  
    snp.matrix-class                        html  
    snp.pre                                 html  
    snp.rhs.tests                           html  
    snpMatrix-internal                      html  
    snpMatrix-package                       html  
    testdata                                html  
    write.snp.matrix                        html  
    wtccc.sample.list                       html  
    xxt                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chopsticks)
Making 'packages.html' ... done