Last data update: 2014.03.03

MCMCpack

Package: MCMCpack
Version: 1.3-6
Date: 2016-4-16
Title: Markov Chain Monte Carlo (MCMC) Package
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Depends: R (>= 2.10.0), coda (>= 0.11-3), MASS, stats
Imports: graphics, grDevices, lattice, methods, utils, mcmc, quantreg
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return coda mcmc objects that can then be summarized
using the coda package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
License: GPL-3
SystemRequirements: gcc (>= 4.0)
URL: http://mcmcpack.berkeley.edu
Packaged: 2016-04-15 00:19:09 UTC; parkjonghee
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2016-04-15 08:32:53

● Cran Task View: Distributions, Multivariate, Psychometrics, Survival
● 3 images, 61 functions, 5 datasets
● Reverse Depends: 19

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MCMCpack' ...
** package 'MCMCpack' successfully unpacked and MD5 sums checked
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking for trunc... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c HMMmultivariateGaussian.cc -o HMMmultivariateGaussian.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c HMMpanelFE.cc -o HMMpanelFE.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c HMMpanelRE.cc -o HMMpanelRE.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCSVDreg.cc -o MCMCSVDreg.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCbinaryChange.cc -o MCMCbinaryChange.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCdynamicEI.cc -o MCMCdynamicEI.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCdynamicIRT1d-b.cc -o MCMCdynamicIRT1d-b.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCdynamicIRT1d.cc -o MCMCdynamicIRT1d.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCfactanal.cc -o MCMCfactanal.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMChierBetaBinom.cc -o MCMChierBetaBinom.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMChierEI.cc -o MCMChierEI.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMChlogit.cc -o MCMChlogit.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMChpoisson.cc -o MCMChpoisson.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMChregress.cc -o MCMChregress.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCirt1d.cc -o MCMCirt1d.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCirtHier1d.cc -o MCMCirtHier1d.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCirtKdHet.cc -o MCMCirtKdHet.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCirtKdRob.cc -o MCMCirtKdRob.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMClogit.cc -o MCMClogit.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMClogituserprior.cc -o MCMClogituserprior.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCmetrop1R.cc -o MCMCmetrop1R.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCmixfactanal.cc -o MCMCmixfactanal.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCmnlMH.cc -o MCMCmnlMH.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCmnlslice.cc -o MCMCmnlslice.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCoprobit.cc -o MCMCoprobit.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCoprobitChange.cc -o MCMCoprobitChange.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCordfactanal.cc -o MCMCordfactanal.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCpoisson.cc -o MCMCpoisson.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCpoissonChange.cc -o MCMCpoissonChange.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCprobit.cc -o MCMCprobit.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCprobitChange.cc -o MCMCprobitChange.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCprobitres.cc -o MCMCprobitres.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCquantreg.cc -o MCMCquantreg.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCregress.cc -o MCMCregress.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCregressChange.cc -o MCMCregressChange.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCresidualBreakAnalysis.cc -o MCMCresidualBreakAnalysis.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c MCMCtobit.cc -o MCMCtobit.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c SSVSquantreg.cc -o SSVSquantreg.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC    -I/usr/local/include    -fpic  -g -O2  -c lecuyer.cc -o lecuyer.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o MCMCpack.so HMMmultivariateGaussian.o HMMpanelFE.o HMMpanelRE.o MCMCSVDreg.o MCMCbinaryChange.o MCMCdynamicEI.o MCMCdynamicIRT1d-b.o MCMCdynamicIRT1d.o MCMCfactanal.o MCMChierBetaBinom.o MCMChierEI.o MCMChlogit.o MCMChpoisson.o MCMChregress.o MCMCirt1d.o MCMCirtHier1d.o MCMCirtKdHet.o MCMCirtKdRob.o MCMClogit.o MCMClogituserprior.o MCMCmetrop1R.o MCMCmixfactanal.o MCMCmnlMH.o MCMCmnlslice.o MCMCoprobit.o MCMCoprobitChange.o MCMCordfactanal.o MCMCpoisson.o MCMCpoissonChange.o MCMCprobit.o MCMCprobitChange.o MCMCprobitres.o MCMCquantreg.o MCMCregress.o MCMCregressChange.o MCMCresidualBreakAnalysis.o MCMCtobit.o SSVSquantreg.o lecuyer.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/MCMCpack/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MCMCpack'
    finding HTML links ... done
    BayesFactor                             html  
    HMMpanelFE                              html  
    HMMpanelRE                              html  
    MCMCSVDreg                              html  
    MCMCbinaryChange                        html  
    MCMCdynamicEI                           html  
    MCMCdynamicIRT1d                        html  
    MCMCfactanal                            html  
    MCMChierEI                              html  
    MCMChlogit                              html  
    MCMChpoisson                            html  
    MCMChregress                            html  
    MCMCirt1d                               html  
    MCMCirtHier1d                           html  
    MCMCirtKd                               html  
    MCMCirtKdHet                            html  
    MCMCirtKdRob                            html  
    MCMClogit                               html  
    MCMCmetrop1R                            html  
    MCMCmixfactanal                         html  
    MCMCmnl                                 html  
    MCMCoprobit                             html  
    MCMCoprobitChange                       html  
    MCMCordfactanal                         html  
    MCMCpoisson                             html  
    MCMCpoissonChange                       html  
    MCMCprobit                              html  
    MCMCprobitChange                        html  
    MCMCquantreg                            html  
    MCMCregress                             html  
    MCMCregressChange                       html  
    MCMCresidualBreakAnalysis               html  
    MCMCtobit                               html  
    MCbinomialbeta                          html  
    MCmultinomdirichlet                     html  
    MCnormalnormal                          html  
    MCpoissongamma                          html  
    Nethvote                                html  
    PErisk                                  html  
    PostProbMod                             html  
    QRSSVSplot                              html  
    QRSSVSsummary                           html  
    Rehnquist                               html  
    SSVSquantreg                            html  
Rd warning: /tmp/RtmpYQcZr7/R.INSTALL5a4244fb45bc/MCMCpack/man/SSVSquantreg.Rd:131: missing file link 'summary.qrssvs'
Rd warning: /tmp/RtmpYQcZr7/R.INSTALL5a4244fb45bc/MCMCpack/man/SSVSquantreg.Rd:132: missing file link 'plot.qrssvs'
    Senate                                  html  
    SupremeCourt                            html  
    choicevar                               html  
    dirichlet                               html  
    dtomog                                  html  
    invgamma                                html  
    iwishart                                html  
    make.breaklist                          html  
    mptable                                 html  
    noncenhypergeom                         html  
    plotChangepoint                         html  
    plotState                               html  
    procrust                                html  
    readscythe                              html  
    testpanelGroupBreak                     html  
    testpanelSubjectBreak                   html  
    tomog                                   html  
    topmodels                               html  
    vech                                    html  
    wishart                                 html  
    writescythe                             html  
    xpnd                                    html  
** building package indices
** testing if installed package can be loaded
* DONE (MCMCpack)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO