mpMap

Package: mpMap
Type: Package
Title: Multi-parent RIL genetic analysis
Version: 1.14
Date: 2012-06-06
Author: Emma Huang
Maintainer: Emma Huang <Emma.Huang@csiro.au>
Description: Tools for constructing linkage maps, reconstructing
haplotypes, estimating linkage disequilibrium and QTL mapping
in multi-parent RIL designs (e.g. MAGIC)
License: GPL-2
LazyLoad: yes
Depends: gdata, seriation, qtl, wgaim
Suggests: aod, asreml, happy.hbrem, Heatplus, MASS, VPdtw, lattice
Collate: 'add3pt.R' 'calc.genoprob2.R' 'calcmpprob.R' 'check-ped.R'
'check-QTL.R' 'clean.mpcross.R' 'cleanmap.R' 'cleanrf.R'
'combine-chr.R' 'combine-ibd.R' 'combine-ld.R' 'combine-rf.R'
'compare-orders.R' 'compute-bnld.R' 'compute-bnrf.R'
'computemap.R' 'convertped.R' 'CR-calcLD.R' 'CR-cross.R'
'CR-estrf.R' 'CR-gen-geno.R' 'fill.R' 'fillmiss.R' 'findqtl2.R'
'fit.mpqtl.R' 'gen4ped.R' 'gen8ped.R' 'generate-error.R'
'generate-obs.R' 'generate-pheno.R' 'getpval.R' 'mapcomp.R'
'maporder.R' 'mp-mapdist.R' 'mpadd.R' 'mpcalcld.R' 'mpcross.R'
'mpestrf.R' 'mpgroup.R' 'mpIM.R' 'mpMap-output.R' 'mporder.R'
'mpprob.R' 'mpsegrat.R' 'nai.R' 'plot.mpcross.R'
'plot.mpprob.R' 'plot.mpqtl.R' 'plotlink.map.R'
'print.mapcomp.R' 'print.mpcross.R' 'print.mpprob.R'
'print.mpqtl.R' 'qtlmap.R' 'read.mpcross.R'
'reorgRIgenoprob2.R' 'sim.mpcross.R' 'sim.mpped.R'
'sim.sigthr.R' 'subset.mpcross.R' 'subset.mpprob.R'
'summary.mpcross.R' 'summary.mpprob.R' 'summary.mpqtl.R'
'supportinterval.R' 'waldTests.R'
Packaged: 2012-06-06 04:42:08 UTC; hua032
Repository: CRAN
Date/Publication: 2012-06-06 05:59:03

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'mpMap' ...
** package 'mpMap' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c 3ptscan.c -o 3ptscan.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c add3pt.c -o add3pt.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c all.c -o all.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c calcLD.c -o calcLD.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c founderprob.c -o founderprob.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pf.c -o pf.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c qsort.c -o qsort.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rngs.c -o rngs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sim.c -o sim.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o mpMap.so 3ptscan.o add3pt.o all.o calcLD.o founderprob.o pf.o qsort.o rngs.o sim.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/mpMap/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'mpMap'
    finding HTML links ... done
    add3pt                                  html  
    clean.mpcross                           html  
    cleanmap                                html  
    compare_orders                          html  
    computemap                              html  
    fillmiss                                html  
    findqtl2                                html  
    fit                                     html  
    mapcomp-all                             html  
    maporder                                html  
    mp-mapdist                              html  
    mpIM                                    html  
    mpMap-internal                          html  
    mpMap-output                            html  
    mpMap-package                           html  
Rd warning: /tmp/RtmpF0NcIv/R.INSTALLea12943f2c6/mpMap/man/mpMap-package.Rd:22: missing file link 'write.mpcross'
    mpadd                                   html  
    mpcalcld                                html  
    mpcross                                 html  
    mpestrf                                 html  
    mpgroup                                 html  
Rd warning: /tmp/RtmpF0NcIv/R.INSTALLea12943f2c6/mpMap/man/mpgroup.Rd:10: missing file link 'mpcross.object'
    mporder                                 html  
Rd warning: /tmp/RtmpF0NcIv/R.INSTALLea12943f2c6/mpMap/man/mporder.Rd:36: missing file link 'fill'
    mpprob                                  html  
    nai                                     html  
    plot.mpcross                            html  
Rd warning: /tmp/RtmpF0NcIv/R.INSTALLea12943f2c6/mpMap/man/plot.mpcross.Rd:43: missing file link 'mpcross.object'
    plot.mpprob                             html  
    plot.mpqtl                              html  
    plotlink.map                            html  
    qtlmap                                  html  
    read.mpcross                            html  
    sim.mpcross                             html  
    sim.mpped                               html  
    sim.sigthr                              html  
    subset.mpcross                          html  
Rd warning: /tmp/RtmpF0NcIv/R.INSTALLea12943f2c6/mpMap/man/subset.mpcross.Rd:44: missing file link 'mpcross.object'
    subset.mpprob                           html  
    summary.mpcross                         html  
    summary.mpprob                          html  
    summary.mpqtl                           html  
    supportinterval                         html  
** building package indices
** testing if installed package can be loaded
* DONE (mpMap)
Making 'packages.html' ... done