MasterBayes

Package: MasterBayes
Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Version: 2.52
Depends: coda, genetics, gtools, kinship2
Date: 2014-12-03
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Description: The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficiency.
License: GPL (>= 2)
Packaged: 2014-12-03 17:54:52 UTC; jhadfiel
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-04 00:43:23

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MasterBayes' ...
** package 'MasterBayes' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c ErrorMat.cc -o ErrorMat.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c LikFunctions.cc -o LikFunctions.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c MCMCped.cc -o MCMCped.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c Read_in_data.cc -o Read_in_data.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c SampD.cc -o SampD.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c SampDomG.cc -o SampDomG.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c SampG.cc -o SampG.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c SampGC.cc -o SampGC.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c SampP.cc -o SampP.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c SampS.cc -o SampS.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c SpecRand.cc -o SpecRand.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c calcX_G.cc -o calcX_G.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c calcX_GD.cc -o calcX_GD.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c calcX_GS.cc -o calcX_GS.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c calcX_Gcervus.cc -o calcX_Gcervus.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c calcX_GcervusD.cc -o calcX_GcervusD.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c calcX_GcervusS.cc -o calcX_GcervusS.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c calcX_Gmm.cc -o calcX_Gmm.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c fillXG.cc -o fillXG.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c legalG.cc -o legalG.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC  -DHAVE_TRUNC  -I/usr/local/include    -fpic  -g -O2  -c mismatches.cc -o mismatches.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o MasterBayes.so ErrorMat.o LikFunctions.o MCMCped.o Read_in_data.o SampD.o SampDomG.o SampG.o SampGC.o SampP.o SampS.o SpecRand.o calcX_G.o calcX_GD.o calcX_GS.o calcX_Gcervus.o calcX_GcervusD.o calcX_GcervusS.o calcX_Gmm.o fillXG.o legalG.o mismatches.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/MasterBayes/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MasterBayes'
    finding HTML links ... done
    GdataPed                                html  
    MCMCped                                 html  
    MLE.beta                                html  
    MLE.ped                                 html  
    MLE.popsize                             html  
    MasterBayes                             html  
    PdataPed                                html  
    WarblerG                                html  
    WarblerP                                html  
    autocorrP                               html  
    beta.loglik                             html  
    consenusG                               html  
    extractA                                html  
    fillX.G                                 html  
    genotype.list                           html  
    genotypeD                               html  
    getXlist                                html  
    insertPed                               html  
    legalG                                  html  
    mismatches                              html  
    modeG                                   html  
    modeP                                   html  
    orderPed                                html  
    popsize.loglik                          html  
    post.pairs                              html  
    priorPed                                html  
    reordXlist                              html  
    simgenotypes                            html  
    simpedigree                             html  
    startPed                                html  
    summary.genotypeD                       html  
    tunePed                                 html  
    varPed                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MasterBayes)
Making 'packages.html' ... done