Can't get Boom 0.5 to install on Ubuntu :(

README.md

Boom! Shake the Room

Yo back up now and give a brother room // The fuse is lit and I'm about to go boom // Mercy mercy mercy me // My life is a cage but on stage I'm free

Okay, so for some reason I can't install Boom on one of our machines ("stat1002", which we'll call "A"). We have a nearly identical machine ("stat1003", which we'll call "B") that I CAN install it on. Other R packages with C++ install just fine -- e.g. Rcpp and dplyr. (Here's Boom's src/Makevars file, by the way.)

Two machines, both alike in dignity

Machine A (the problematic one)

sessionInfo()
# R version 3.2.3 (2015-12-10)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 14.04.4 LTS

g++ --version
# g++ (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4
make --version
# GNU Make 3.81
ar --version
# GNU ar (GNU Binutils for Ubuntu) 2.24

Update

My coworker Erik noticed that there's a file (/usr/share/R/debian/r-cran.mk) that's in A's R installation that isn't in B's. Maybe that has something to do with it?

Machine B (the OK one)

sessionInfo()
# R version 3.2.3 (2015-12-10)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 14.04.4 LTS

g++ --version
# g++ (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4
make --version
# GNU Make 3.81
ar --version
# GNU ar (GNU Binutils for Ubuntu) 2.24

Installing

boom_install_b.log is the log of what happens when I (successfully) install Boom from CRAN on machine B.

Attempt 1

boom_install_a-1.log is the log of what happens when I try to install Boom from CRAN on machine A.

Attempt 2

After reading some StackOverflow threads (e.g. this one and this one), I made a ~/.R/Makevars file with the following lines:

CXX=g++-4.8
CXX1X=g++-4.8

But there were issues with C++11 support not activating (see boom_install_a-2.log).

Attempt 3

So I changed ~/.R/Makevars to have:

CXX=g++-4.8
CXX1X=g++-4.8
CXX1XFLAGS=-std=c++11

which yielded the partially successful boom_install_a-3.log, except for some reason there's a line break that forces -o to be taken as a command. So, like, whaaaaaaaat?

This is really weird because everything else installs perfectly OK without any make variable setting -- see Rcpp_reinstall_a.log, where I successfully reinstall Rcpp after commenting out the lines in ~/.R/Makevars o_O

Then I went into Boom's source, edited the src/Makevars#98 to have $(shell echo $^) because I read that shell removes newlines^{1, 2} and tried different variations of that, but for whatever reason "-o Boom.so" still went to a new line :/

It's so frustrating D: I don't know what else to do! Tic-tic-tic-tic Boom!

Attempt 4

Drew pointed out that:

The third error isn't a newline problem. It's trying to generate Boom.so but $CXX is blank again at that point for some reason. (https://twitter.com/wrathematics/status/784458657471819780)

And suggested to try setting the first line:

all: $(SHLIB)
$(SHLIB): libboom.a

and to "try setting CXX in Makevars over .R/M[akevars]" (https://twitter.com/wrathematics/status/784458928881098753)

So I commented out the variable settings in ~/.R/Makevars and changed src/Makevars to start with:

all: $(SHLIB)
$(SHLIB): libboom.a

CXX=g++-4.8
CXX1X=g++-4.8
CXX_STD = CXX11
CXX1XFLAGS=-std=c++11

which yields the yet-again-only-partially-successful boom_install_a-4.log. Maybe this /usr/share/R/debian/r-cran.mk file that is present on machine A but not B has something to with it?

boom_install_a-1.log

Installing package into ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/Boom_0.5.tar.gz'
Content type 'application/x-gzip' length 1061942 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘Boom’ ...
** package ‘Boom’ successfully unpacked and MD5 sums checked
** libs
I/usr/share/R/include -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"      -c Models/Bart/Bart.cpp -o Models/Bart/Bart.o
/bin/bash: I/usr/share/R/include: No such file or directory
make: [Models/Bart/Bart.o] Error 127 (ignored)
...
I/usr/share/R/include -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"      -c cpputil/trim_white_space.cpp -o cpputil/trim_white_space.o
/bin/bash: I/usr/share/R/include: No such file or directory
make: [cpputil/trim_white_space.o] Error 127 (ignored)
ar rc libboom.a Models/Bart/Bart.o Models/Bart/GaussianBartModel.o Models/Bart/GaussianLinearBartModel.o Models/Bart/LogitBartModel.o Models/Bart/PoissonBartModel.o Models/Bart/ProbitBartModel.o Models/Bart/ResidualRegressionData.o Models/Bart/PosteriorSamplers/BartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.o Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.o Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.o Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.o distributions/BinomialDistribution.o distributions/BoundedAdaptiveRejectionSampler.o distributions/DoublyBoundedAdaptiveRejectionSampler.o distributions/Markov.o distributions/Rmath_dist.o distributions/Tn2Sampler.o distributions/Wishart.o distributions/dirichlet.o distributions/extreme_value.o distributions/inverse_gaussian.o distributions/matrix_normal.o distributions/mvn.o distributions/mvt.o distributions/random_cor.o distributions/random_int.o distributions/rlexp.o distributions/rmulti.o distributions/rng.o distributions/rtriangle.o distributions/student_fix.o distributions/trun_exp.o distributions/trun_gamma.o distributions/trun_logit.o distributions/trun_norm.o distributions/usp.o Models/Glm/AggregatedRegressionModel.o Models/Glm/BinomialLogitModel.o Models/Glm/BinomialProbitModel.o Models/Glm/BinomialRegressionData.o Models/Glm/ChoiceData.o Models/Glm/CumulativeLogitModel.o Models/Glm/CumulativeProbitModel.o Models/Glm/GammaRegressionModel.o Models/Glm/Glm.o Models/Glm/GlmCoefs.o Models/Glm/HierarchicalPoissonRegression.o Models/Glm/LogisticRegressionModel.o Models/Glm/MultinomialLogitModel.o Models/Glm/MultinomialProbitModel.o Models/Glm/MvReg2.o Models/Glm/MvnGivenX.o Models/Glm/MvnGivenXandSigma.o Models/Glm/MvtRegModel.o Models/Glm/OrdinalCutpointModel.o Models/Glm/PoissonRegressionData.o Models/Glm/PoissonRegressionModel.o Models/Glm/ProbitRegression.o Models/Glm/RegressionModel.o Models/Glm/TRegression.o Models/Glm/VariableSelectionPrior.o Models/Glm/WeightedRegressionModel.o Models/Glm/ZeroInflatedGammaRegression.o Models/Glm/ZeroInflatedLognormalRegression.o Models/Glm/ZeroInflatedPoissonRegression.o Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.o Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.o Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.o Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.o Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.o Models/Glm/PosteriorSamplers/BregVsSampler.o Models/Glm/PosteriorSamplers/CumulativeLogitSampler.o Models/Glm/PosteriorSamplers/CumulativeProbitSampler.o Models/Glm/PosteriorSamplers/DAFE_MLM.o Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/LogitSampler.o Models/Glm/PosteriorSamplers/LogitSamplerBma.o Models/Glm/PosteriorSamplers/MLAuxMixSampler.o Models/Glm/PosteriorSamplers/MLVS.o Models/Glm/PosteriorSamplers/MLVS_data_imputer.o Models/Glm/PosteriorSamplers/MlogitRwm.o Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.o Models/Glm/PosteriorSamplers/MnpBetaSampler.o Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.o Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/MvRegSampler.o Models/Glm/PosteriorSamplers/MvtRegSampler.o Models/Glm/PosteriorSamplers/NormalMixtureApproximation.o Models/Glm/PosteriorSamplers/PartRegSampler.o Models/Glm/PosteriorSamplers/PoissonDataImputer.o Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/ProbitRegressionSampler.o Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/RegressionConjSampler.o Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.o Models/Glm/PosteriorSamplers/SpikeSlabSampler.o Models/Glm/PosteriorSamplers/TDataImputer.o Models/Glm/PosteriorSamplers/TRegressionSampler.o Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/VsPriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/draw_logit_lambda.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o Models/Hierarchical/HierarchicalDirichletModel.o Models/Hierarchical/HierarchicalGammaModel.o Models/Hierarchical/HierarchicalPoissonModel.o Models/Hierarchical/HierarchicalZeroInflatedGammaModel.o Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.o Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.o Models/HMM/HMM2.o Models/HMM/HealthStateModel.o Models/HMM/HmmDataImputer.o Models/HMM/HmmFilter.o Models/HMM/hmm_tools.o Models/HMM/Clickstream/Event.o Models/HMM/Clickstream/NestedHmm.o Models/HMM/Clickstream/Session.o Models/HMM/Clickstream/Stream.o Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.o Models/HMM/PosteriorSamplers/HmmPosteriorSampler.o Models/IRT/DafePcrDataImputer.o Models/IRT/DafePcrItemSampler.o Models/IRT/DafePcrRwmItemSampler.o Models/IRT/DafePcrRwmSubject.o Models/IRT/DafePcrSubject.o Models/IRT/IRT.o Models/IRT/IrtModel.o Models/IRT/Item.o Models/IRT/PartialCreditModel.o Models/IRT/Subject.o Models/IRT/SubjectPrior.o Models/IRT/SubjectSliceSampler.o LinAlg/Array.o LinAlg/Array3.o LinAlg/ArrayIterator.o LinAlg/Cholesky.o LinAlg/CorrelationMatrix.o LinAlg/DiagonalMatrix.o LinAlg/Eigen.o LinAlg/Givens.o LinAlg/Kronecker.o LinAlg/LU.o LinAlg/LinAlgExceptions.o LinAlg/Matrix.o LinAlg/MatrixPartition.o LinAlg/QR.o LinAlg/SVD.o LinAlg/SWEEP.o LinAlg/Selector.o LinAlg/SpdMatrix.o LinAlg/SubMatrix.o LinAlg/Vector.o LinAlg/VectorView.o LinAlg/blas.o LinAlg/stack_columns.o math/cephes/chbevl.o math/cephes/dawsn.o math/cephes/ei.o math/cephes/expn.o math/cephes/fac.o math/cephes/fresnl.o math/cephes/planck.o math/cephes/polevl.o math/cephes/polylog.o math/cephes/powi.o math/cephes/rgamma.o math/cephes/shichi.o math/cephes/sici.o math/cephes/spence.o math/cephes/zeta.o math/cephes/zetac.o Models/Mixtures/ConditionalFiniteMixtureModel.o Models/Mixtures/DirichletProcessMvnModel.o Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.o Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.o Models/BetaBinomialModel.o Models/BetaModel.o Models/BinomialModel.o Models/CategoricalData.o Models/ChisqModel.o Models/CompositeData.o Models/CompositeModel.o Models/CompositeVectorModel.o Models/ConstrainedVectorParams.o Models/DataTypes.o Models/DirichletModel.o Models/DiscreteUniformModel.o Models/ExponentialModel.o Models/FiniteMixtureModel.o Models/GammaModel.o Models/GaussianModel.o Models/GaussianModelBase.o Models/GaussianModelGivenSigma.o Models/IndependentMvnModel.o Models/IndependentMvnModelGivenScalarSigma.o Models/LognormalModel.o Models/MarginallyUniformCorrelationModel.o Models/MarkovModel.o Models/ModelTypes.o Models/MultinomialModel.o Models/MvnBase.o Models/MvnGivenScalarSigma.o Models/MvnGivenSigma.o Models/MvnModel.o Models/MvtModel.o Models/ParamTypes.o Models/PoissonGammaModel.o Models/PoissonModel.o Models/ProductDirichletModel.o Models/ScaledChisqModel.o Models/SpdData.o Models/SpdModel.o Models/SpdParams.o Models/Sufstat.o Models/TruncatedGammaModel.o Models/UniformCorrelationModel.o Models/UniformModel.o Models/UniformShrinkagePriorModel.o Models/WeightedGaussianSuf.o Models/WeightedMvnModel.o Models/WishartModel.o Models/ZeroInflatedGammaModel.o Models/ZeroInflatedLognormalModel.o Models/ZeroInflatedPoissonModel.o Models/ZeroMeanGaussianModel.o Models/ZeroMeanMvnModel.o Models/Policies/CompositeParamPolicy.o Models/Policies/ManyParamPolicy.o Models/Policies/MixtureDataPolicy.o Models/Policies/NullParamPolicy.o Models/Policies/PriorPolicy.o Models/PosteriorSamplers/AbsorbingMarkovConjSampler.o Models/PosteriorSamplers/BetaBinomialPosteriorSampler.o Models/PosteriorSamplers/BetaBinomialSampler.o Models/PosteriorSamplers/BetaPosteriorSampler.o Models/PosteriorSamplers/CompositeModelSampler.o Models/PosteriorSamplers/CompositeSampler.o Models/PosteriorSamplers/CorrelationSampler.o Models/PosteriorSamplers/DirichletPosteriorSampler.o Models/PosteriorSamplers/ExchangeableDirichletSampler.o Models/PosteriorSamplers/ExponentialGammaSampler.o Models/PosteriorSamplers/FixedProbBinomialSampler.o Models/PosteriorSamplers/GammaPosteriorSampler.o Models/PosteriorSamplers/GaussianConjSampler.o Models/PosteriorSamplers/GaussianMeanSampler.o Models/PosteriorSamplers/GaussianVarSampler.o Models/PosteriorSamplers/GenericGaussianVarianceSampler.o Models/PosteriorSamplers/IndependentMvnConjSampler.o Models/PosteriorSamplers/IndependentMvnVarSampler.o Models/PosteriorSamplers/MarkovConjSampler.o Models/PosteriorSamplers/MarkovConjShrinkageSampler.o Models/PosteriorSamplers/MultinomialDirichletSampler.o Models/PosteriorSamplers/MvnConjSampler.o Models/PosteriorSamplers/MvnIndependentVarianceSampler.o Models/PosteriorSamplers/MvnMeanSampler.o Models/PosteriorSamplers/MvnVarSampler.o Models/PosteriorSamplers/PoissonGammaPosteriorSampler.o Models/PosteriorSamplers/PoissonGammaSampler.o Models/PosteriorSamplers/PosteriorSampler.o Models/PosteriorSamplers/ProductDirichletPosteriorSampler.o Models/PosteriorSamplers/SepStratSampler.o Models/PosteriorSamplers/SharedSigsqSampler.o Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedPoissonSampler.o Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.o numopt/Brent.o numopt/Integral.o numopt/Negate.o numopt/NelderMead.o numopt/NumericalDerivatives.o numopt/Powell.o numopt/ScalarLaplaceApproximation.o numopt/ScalarNewtonMax.o numopt/bfgs.o numopt/conj_grad.o numopt/initialize_derivatives.o numopt/max_nd.o numopt/nelder_mead.o numopt/newton.o numopt/simulated_annealing.o Models/PointProcess/BoundedPoissonProcessSimulator.o Models/PointProcess/CosinePoissonProcess.o Models/PointProcess/HomogeneousPoissonProcess.o Models/PointProcess/MarkovModulatedPoissonProcess.o Models/PointProcess/PointProcess.o Models/PointProcess/PoissonClusterProcess.o Models/PointProcess/WeeklyCyclePoissonProcess.o Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.o boom_r_tools.o create_mixture_component.o create_point_process.o create_poisson_cluster_components.o create_poisson_process.o create_state_model.o determine_nthreads.o extract_mixture_data.o handle_exception.o list_io.o parse_model_formula.o print_R_timestamp.o prior_specification.o seed_rng_from_R.o spike_slab_prior.o Bmath/bd0.o Bmath/beta.o Bmath/chebyshev.o Bmath/choose.o Bmath/d1mach.o Bmath/dbeta.o Bmath/dbinom.o Bmath/dcauchy.o Bmath/dchisq.o Bmath/dexp.o Bmath/df.o Bmath/dgamma.o Bmath/dgeom.o Bmath/dhyper.o Bmath/dlnorm.o Bmath/dlogis.o Bmath/dnbeta.o Bmath/dnbinom.o Bmath/dnchisq.o Bmath/dnorm.o Bmath/dpois.o Bmath/dt.o Bmath/dunif.o Bmath/dweibull.o Bmath/fprec.o Bmath/fround.o Bmath/fsign.o Bmath/ftrunc.o Bmath/gamma_cody.o Bmath/gammalims.o Bmath/i1mach.o Bmath/lbeta.o Bmath/lgammacor.o Bmath/mathlib_error.o Bmath/mlutils.o Bmath/pbeta.o Bmath/pbinom.o Bmath/pcauchy.o Bmath/pchisq.o Bmath/pexp.o Bmath/pf.o Bmath/pgamma.o Bmath/pgeom.o Bmath/phyper.o Bmath/plnorm.o Bmath/plogis.o Bmath/pnbeta.o Bmath/pnbinom.o Bmath/pnchisq.o Bmath/pnf.o Bmath/pnorm.o Bmath/pnt.o Bmath/polygamma.o Bmath/ppois.o Bmath/pt.o Bmath/ptukey.o Bmath/punif.o Bmath/pweibull.o Bmath/qbeta.o Bmath/qbinom.o Bmath/qcauchy.o Bmath/qchisq.o Bmath/qexp.o Bmath/qf.o Bmath/qgamma.o Bmath/qgeom.o Bmath/qhyper.o Bmath/qlnorm.o Bmath/qlogis.o Bmath/qnbinom.o Bmath/qnchisq.o Bmath/qnorm.o Bmath/qpois.o Bmath/qt.o Bmath/qtukey.o Bmath/qunif.o Bmath/qweibull.o Bmath/rbeta.o Bmath/rbinom.o Bmath/rcauchy.o Bmath/rchisq.o Bmath/rexp.o Bmath/rf.o Bmath/rgamma.o Bmath/rgeom.o Bmath/rhyper.o Bmath/rlnorm.o Bmath/rlogis.o Bmath/rmultinom.o Bmath/rnbinom.o Bmath/rnchisq.o Bmath/rnorm.o Bmath/rpois.o Bmath/rt.o Bmath/runif.o Bmath/rweibull.o Bmath/sexp.o Bmath/sign.o Bmath/snorm.o Bmath/stirlerr.o Bmath/toms708.o Bmath/unif_rand.o Samplers/ARMS.o Samplers/DirectProposal.o Samplers/ImportanceResampler.o Samplers/MH_Proposals.o Samplers/MetropolisHastings.o Samplers/MoveAccounting.o Samplers/RejectionSampler.o Samplers/Sampler.o Samplers/ScalarAdaptiveRejectionSampler.o Samplers/ScalarLangevinSampler.o Samplers/ScalarSliceSampler.o Samplers/SliceSampler.o Samplers/TIM.o Samplers/UnivariateLangevinSampler.o Samplers/UnivariateSliceSampler.o Samplers/Gilks/arms.o stats/Bspline.o stats/ChiSquareTest.o stats/DataTable.o stats/Design.o stats/ECDF.o stats/FreqDist.o stats/IQagent.o stats/NaturalSpline.o stats/Resampler.o stats/Spline.o stats/compare_binomial_proportions.o stats/compare_predictions.o stats/diff.o stats/moments.o stats/regression.o stats/simple_random_sample.o Models/StateSpace/AggregatedStateSpaceRegression.o Models/StateSpace/StateSpaceLogitModel.o Models/StateSpace/StateSpaceModel.o Models/StateSpace/StateSpaceModelBase.o Models/StateSpace/StateSpaceNormalMixture.o Models/StateSpace/StateSpacePoissonModel.o Models/StateSpace/StateSpaceRegressionModel.o Models/StateSpace/StateSpaceStudentRegressionModel.o Models/StateSpace/Filters/KalmanTools.o Models/StateSpace/Filters/SparseKalmanTools.o Models/StateSpace/Filters/SparseMatrix.o Models/StateSpace/Filters/SparseVector.o Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.o Models/StateSpace/StateModels/ArStateModel.o Models/StateSpace/StateModels/DynamicRegressionStateModel.o Models/StateSpace/StateModels/Holiday.o Models/StateSpace/StateModels/LocalLevelStateModel.o Models/StateSpace/StateModels/LocalLinearTrend.o Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.o Models/StateSpace/StateModels/RandomWalkHolidayStateModel.o Models/StateSpace/StateModels/RegressionStateModel.o Models/StateSpace/StateModels/SeasonalStateModel.o Models/StateSpace/StateModels/StateModel.o Models/StateSpace/StateModels/StudentLocalLinearTrend.o Models/StateSpace/StateModels/TrigStateModel.o TargetFun/JacobianChecker.o TargetFun/LogPost.o TargetFun/ScalarLogpostTF.o TargetFun/TargetFun.o TargetFun/Transformation.o Models/TimeSeries/ArModel.o Models/TimeSeries/NonzeroMeanAr1Model.o Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.o Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.o Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.o cpputil/Constants.o cpputil/Date.o cpputil/DateTime.o cpputil/DefaultVnames.o cpputil/LongString.o cpputil/OutputTable.o cpputil/ParamHolder.o cpputil/Polynomial.o cpputil/Redirector.o cpputil/apply_permutation.o cpputil/cat_string.o cpputil/compare_vector_bool.o cpputil/get_date.o cpputil/gll.o cpputil/infinity.o cpputil/is_all_white.o cpputil/is_numeric.o cpputil/legalize_file_name.o cpputil/lse.o cpputil/parse_range.o cpputil/print_columns.o cpputil/read_file.o cpputil/rep.o cpputil/replace_all.o cpputil/report_error.o cpputil/safelog.o cpputil/split.o cpputil/split_delimited.o cpputil/split_string.o cpputil/str2d.o cpputil/strip.o cpputil/strip_path.o cpputil/strip_white_space.o cpputil/substring_delimited.o cpputil/trim_white_space.o
ar: Models/Bart/Bart.o: No such file or directory
make: *** [libboom.a] Error 1
ERROR: compilation failed for package ‘Boom’
* removing ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/Boom’

The downloaded source packages are in
	‘/tmp/RtmpRsJISZ/downloaded_packages’
Warning message:
In install.packages("Boom") :
  installation of package ‘Boom’ had non-zero exit status

boom_install_a-2.log

Installing package into ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/Boom_0.5.tar.gz'
Content type 'application/x-gzip' length 1061942 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘Boom’ ...
** package ‘Boom’ successfully unpacked and MD5 sums checked
** libs
g++-4.8  -I/usr/share/R/include -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"      -c Models/Bart/Bart.cpp -o Models/Bart/Bart.o
In file included from /usr/include/c++/4.8/initializer_list:36:0,
                 from ../inst/include/LinAlg/Vector.hpp:23,
                 from ../inst/include/LinAlg/VectorView.hpp:27,
                 from ../inst/include/LinAlg/Matrix.hpp:22,
                 from ../inst/include/LinAlg/SubMatrix.hpp:20,
                 from ../inst/include/Models/Bart/Bart.hpp:24,
                 from Models/Bart/Bart.cpp:24:
/usr/include/c++/4.8/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
In file included from ../inst/include/LinAlg/VectorView.hpp:27:0,
                 from ../inst/include/LinAlg/Matrix.hpp:22,
                 from ../inst/include/LinAlg/SubMatrix.hpp:20,
                 from ../inst/include/Models/Bart/Bart.hpp:24,
                 from Models/Bart/Bart.cpp:24:
../inst/include/LinAlg/Vector.hpp:62:18: error: ‘initializer_list’ in namespace ‘std’ does not name a type
     Vector(const std::initializer_list<double> &init);
                  ^
../inst/include/LinAlg/Vector.hpp:62:23: error: ISO C++ forbids declaration of ‘parameter’ with no type [-fpermissive]
     Vector(const std::initializer_list<double> &init);
                       ^
../inst/include/LinAlg/Vector.hpp:62:39: error: expected ‘,’ or ‘...’ before ‘<’ token
     Vector(const std::initializer_list<double> &init);
                                       ^
../inst/include/LinAlg/Vector.hpp:78:19: error: expected ‘,’ or ‘...’ before ‘&&’ token
     Vector(Vector &&v) = default;
                   ^
../inst/include/LinAlg/Vector.hpp:78:26: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
     Vector(Vector &&v) = default;
                          ^
...
make: *** [Models/Bart/Bart.o] Error 1
ERROR: compilation failed for package ‘Boom’
* removing ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/Boom’

The downloaded source packages are in
	‘/tmp/Rtmpa7da4w/downloaded_packages’
Warning message:
In install.packages("Boom") :
  installation of package ‘Boom’ had non-zero exit status

boom_install_a-3.log

Installing package into ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/Boom_0.5.tar.gz'
Content type 'application/x-gzip' length 1061942 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘Boom’ ...
** package ‘Boom’ successfully unpacked and MD5 sums checked
** libs
g++-4.8  -I/usr/share/R/include -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"     -std=c++11 -c Models/Bart/Bart.cpp -o Models/Bart/Bart.o
...
g++-4.8  -I/usr/share/R/include -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"     -std=c++11 -c cpputil/trim_white_space.cpp -o cpputil/trim_white_space.o
ar rc libboom.a Models/Bart/Bart.o Models/Bart/GaussianBartModel.o Models/Bart/GaussianLinearBartModel.o Models/Bart/LogitBartModel.o Models/Bart/PoissonBartModel.o Models/Bart/ProbitBartModel.o Models/Bart/ResidualRegressionData.o Models/Bart/PosteriorSamplers/BartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.o Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.o Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.o Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.o distributions/BinomialDistribution.o distributions/BoundedAdaptiveRejectionSampler.o distributions/DoublyBoundedAdaptiveRejectionSampler.o distributions/Markov.o distributions/Rmath_dist.o distributions/Tn2Sampler.o distributions/Wishart.o distributions/dirichlet.o distributions/extreme_value.o distributions/inverse_gaussian.o distributions/matrix_normal.o distributions/mvn.o distributions/mvt.o distributions/random_cor.o distributions/random_int.o distributions/rlexp.o distributions/rmulti.o distributions/rng.o distributions/rtriangle.o distributions/student_fix.o distributions/trun_exp.o distributions/trun_gamma.o distributions/trun_logit.o distributions/trun_norm.o distributions/usp.o Models/Glm/AggregatedRegressionModel.o Models/Glm/BinomialLogitModel.o Models/Glm/BinomialProbitModel.o Models/Glm/BinomialRegressionData.o Models/Glm/ChoiceData.o Models/Glm/CumulativeLogitModel.o Models/Glm/CumulativeProbitModel.o Models/Glm/GammaRegressionModel.o Models/Glm/Glm.o Models/Glm/GlmCoefs.o Models/Glm/HierarchicalPoissonRegression.o Models/Glm/LogisticRegressionModel.o Models/Glm/MultinomialLogitModel.o Models/Glm/MultinomialProbitModel.o Models/Glm/MvReg2.o Models/Glm/MvnGivenX.o Models/Glm/MvnGivenXandSigma.o Models/Glm/MvtRegModel.o Models/Glm/OrdinalCutpointModel.o Models/Glm/PoissonRegressionData.o Models/Glm/PoissonRegressionModel.o Models/Glm/ProbitRegression.o Models/Glm/RegressionModel.o Models/Glm/TRegression.o Models/Glm/VariableSelectionPrior.o Models/Glm/WeightedRegressionModel.o Models/Glm/ZeroInflatedGammaRegression.o Models/Glm/ZeroInflatedLognormalRegression.o Models/Glm/ZeroInflatedPoissonRegression.o Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.o Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.o Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.o Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.o Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.o Models/Glm/PosteriorSamplers/BregVsSampler.o Models/Glm/PosteriorSamplers/CumulativeLogitSampler.o Models/Glm/PosteriorSamplers/CumulativeProbitSampler.o Models/Glm/PosteriorSamplers/DAFE_MLM.o Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/LogitSampler.o Models/Glm/PosteriorSamplers/LogitSamplerBma.o Models/Glm/PosteriorSamplers/MLAuxMixSampler.o Models/Glm/PosteriorSamplers/MLVS.o Models/Glm/PosteriorSamplers/MLVS_data_imputer.o Models/Glm/PosteriorSamplers/MlogitRwm.o Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.o Models/Glm/PosteriorSamplers/MnpBetaSampler.o Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.o Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/MvRegSampler.o Models/Glm/PosteriorSamplers/MvtRegSampler.o Models/Glm/PosteriorSamplers/NormalMixtureApproximation.o Models/Glm/PosteriorSamplers/PartRegSampler.o Models/Glm/PosteriorSamplers/PoissonDataImputer.o Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/ProbitRegressionSampler.o Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/RegressionConjSampler.o Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.o Models/Glm/PosteriorSamplers/SpikeSlabSampler.o Models/Glm/PosteriorSamplers/TDataImputer.o Models/Glm/PosteriorSamplers/TRegressionSampler.o Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/VsPriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/draw_logit_lambda.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o Models/Hierarchical/HierarchicalDirichletModel.o Models/Hierarchical/HierarchicalGammaModel.o Models/Hierarchical/HierarchicalPoissonModel.o Models/Hierarchical/HierarchicalZeroInflatedGammaModel.o Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.o Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.o Models/HMM/HMM2.o Models/HMM/HealthStateModel.o Models/HMM/HmmDataImputer.o Models/HMM/HmmFilter.o Models/HMM/hmm_tools.o Models/HMM/Clickstream/Event.o Models/HMM/Clickstream/NestedHmm.o Models/HMM/Clickstream/Session.o Models/HMM/Clickstream/Stream.o Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.o Models/HMM/PosteriorSamplers/HmmPosteriorSampler.o Models/IRT/DafePcrDataImputer.o Models/IRT/DafePcrItemSampler.o Models/IRT/DafePcrRwmItemSampler.o Models/IRT/DafePcrRwmSubject.o Models/IRT/DafePcrSubject.o Models/IRT/IRT.o Models/IRT/IrtModel.o Models/IRT/Item.o Models/IRT/PartialCreditModel.o Models/IRT/Subject.o Models/IRT/SubjectPrior.o Models/IRT/SubjectSliceSampler.o LinAlg/Array.o LinAlg/Array3.o LinAlg/ArrayIterator.o LinAlg/Cholesky.o LinAlg/CorrelationMatrix.o LinAlg/DiagonalMatrix.o LinAlg/Eigen.o LinAlg/Givens.o LinAlg/Kronecker.o LinAlg/LU.o LinAlg/LinAlgExceptions.o LinAlg/Matrix.o LinAlg/MatrixPartition.o LinAlg/QR.o LinAlg/SVD.o LinAlg/SWEEP.o LinAlg/Selector.o LinAlg/SpdMatrix.o LinAlg/SubMatrix.o LinAlg/Vector.o LinAlg/VectorView.o LinAlg/blas.o LinAlg/stack_columns.o math/cephes/chbevl.o math/cephes/dawsn.o math/cephes/ei.o math/cephes/expn.o math/cephes/fac.o math/cephes/fresnl.o math/cephes/planck.o math/cephes/polevl.o math/cephes/polylog.o math/cephes/powi.o math/cephes/rgamma.o math/cephes/shichi.o math/cephes/sici.o math/cephes/spence.o math/cephes/zeta.o math/cephes/zetac.o Models/Mixtures/ConditionalFiniteMixtureModel.o Models/Mixtures/DirichletProcessMvnModel.o Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.o Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.o Models/BetaBinomialModel.o Models/BetaModel.o Models/BinomialModel.o Models/CategoricalData.o Models/ChisqModel.o Models/CompositeData.o Models/CompositeModel.o Models/CompositeVectorModel.o Models/ConstrainedVectorParams.o Models/DataTypes.o Models/DirichletModel.o Models/DiscreteUniformModel.o Models/ExponentialModel.o Models/FiniteMixtureModel.o Models/GammaModel.o Models/GaussianModel.o Models/GaussianModelBase.o Models/GaussianModelGivenSigma.o Models/IndependentMvnModel.o Models/IndependentMvnModelGivenScalarSigma.o Models/LognormalModel.o Models/MarginallyUniformCorrelationModel.o Models/MarkovModel.o Models/ModelTypes.o Models/MultinomialModel.o Models/MvnBase.o Models/MvnGivenScalarSigma.o Models/MvnGivenSigma.o Models/MvnModel.o Models/MvtModel.o Models/ParamTypes.o Models/PoissonGammaModel.o Models/PoissonModel.o Models/ProductDirichletModel.o Models/ScaledChisqModel.o Models/SpdData.o Models/SpdModel.o Models/SpdParams.o Models/Sufstat.o Models/TruncatedGammaModel.o Models/UniformCorrelationModel.o Models/UniformModel.o Models/UniformShrinkagePriorModel.o Models/WeightedGaussianSuf.o Models/WeightedMvnModel.o Models/WishartModel.o Models/ZeroInflatedGammaModel.o Models/ZeroInflatedLognormalModel.o Models/ZeroInflatedPoissonModel.o Models/ZeroMeanGaussianModel.o Models/ZeroMeanMvnModel.o Models/Policies/CompositeParamPolicy.o Models/Policies/ManyParamPolicy.o Models/Policies/MixtureDataPolicy.o Models/Policies/NullParamPolicy.o Models/Policies/PriorPolicy.o Models/PosteriorSamplers/AbsorbingMarkovConjSampler.o Models/PosteriorSamplers/BetaBinomialPosteriorSampler.o Models/PosteriorSamplers/BetaBinomialSampler.o Models/PosteriorSamplers/BetaPosteriorSampler.o Models/PosteriorSamplers/CompositeModelSampler.o Models/PosteriorSamplers/CompositeSampler.o Models/PosteriorSamplers/CorrelationSampler.o Models/PosteriorSamplers/DirichletPosteriorSampler.o Models/PosteriorSamplers/ExchangeableDirichletSampler.o Models/PosteriorSamplers/ExponentialGammaSampler.o Models/PosteriorSamplers/FixedProbBinomialSampler.o Models/PosteriorSamplers/GammaPosteriorSampler.o Models/PosteriorSamplers/GaussianConjSampler.o Models/PosteriorSamplers/GaussianMeanSampler.o Models/PosteriorSamplers/GaussianVarSampler.o Models/PosteriorSamplers/GenericGaussianVarianceSampler.o Models/PosteriorSamplers/IndependentMvnConjSampler.o Models/PosteriorSamplers/IndependentMvnVarSampler.o Models/PosteriorSamplers/MarkovConjSampler.o Models/PosteriorSamplers/MarkovConjShrinkageSampler.o Models/PosteriorSamplers/MultinomialDirichletSampler.o Models/PosteriorSamplers/MvnConjSampler.o Models/PosteriorSamplers/MvnIndependentVarianceSampler.o Models/PosteriorSamplers/MvnMeanSampler.o Models/PosteriorSamplers/MvnVarSampler.o Models/PosteriorSamplers/PoissonGammaPosteriorSampler.o Models/PosteriorSamplers/PoissonGammaSampler.o Models/PosteriorSamplers/PosteriorSampler.o Models/PosteriorSamplers/ProductDirichletPosteriorSampler.o Models/PosteriorSamplers/SepStratSampler.o Models/PosteriorSamplers/SharedSigsqSampler.o Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedPoissonSampler.o Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.o numopt/Brent.o numopt/Integral.o numopt/Negate.o numopt/NelderMead.o numopt/NumericalDerivatives.o numopt/Powell.o numopt/ScalarLaplaceApproximation.o numopt/ScalarNewtonMax.o numopt/bfgs.o numopt/conj_grad.o numopt/initialize_derivatives.o numopt/max_nd.o numopt/nelder_mead.o numopt/newton.o numopt/simulated_annealing.o Models/PointProcess/BoundedPoissonProcessSimulator.o Models/PointProcess/CosinePoissonProcess.o Models/PointProcess/HomogeneousPoissonProcess.o Models/PointProcess/MarkovModulatedPoissonProcess.o Models/PointProcess/PointProcess.o Models/PointProcess/PoissonClusterProcess.o Models/PointProcess/WeeklyCyclePoissonProcess.o Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.o boom_r_tools.o create_mixture_component.o create_point_process.o create_poisson_cluster_components.o create_poisson_process.o create_state_model.o determine_nthreads.o extract_mixture_data.o handle_exception.o list_io.o parse_model_formula.o print_R_timestamp.o prior_specification.o seed_rng_from_R.o spike_slab_prior.o Bmath/bd0.o Bmath/beta.o Bmath/chebyshev.o Bmath/choose.o Bmath/d1mach.o Bmath/dbeta.o Bmath/dbinom.o Bmath/dcauchy.o Bmath/dchisq.o Bmath/dexp.o Bmath/df.o Bmath/dgamma.o Bmath/dgeom.o Bmath/dhyper.o Bmath/dlnorm.o Bmath/dlogis.o Bmath/dnbeta.o Bmath/dnbinom.o Bmath/dnchisq.o Bmath/dnorm.o Bmath/dpois.o Bmath/dt.o Bmath/dunif.o Bmath/dweibull.o Bmath/fprec.o Bmath/fround.o Bmath/fsign.o Bmath/ftrunc.o Bmath/gamma_cody.o Bmath/gammalims.o Bmath/i1mach.o Bmath/lbeta.o Bmath/lgammacor.o Bmath/mathlib_error.o Bmath/mlutils.o Bmath/pbeta.o Bmath/pbinom.o Bmath/pcauchy.o Bmath/pchisq.o Bmath/pexp.o Bmath/pf.o Bmath/pgamma.o Bmath/pgeom.o Bmath/phyper.o Bmath/plnorm.o Bmath/plogis.o Bmath/pnbeta.o Bmath/pnbinom.o Bmath/pnchisq.o Bmath/pnf.o Bmath/pnorm.o Bmath/pnt.o Bmath/polygamma.o Bmath/ppois.o Bmath/pt.o Bmath/ptukey.o Bmath/punif.o Bmath/pweibull.o Bmath/qbeta.o Bmath/qbinom.o Bmath/qcauchy.o Bmath/qchisq.o Bmath/qexp.o Bmath/qf.o Bmath/qgamma.o Bmath/qgeom.o Bmath/qhyper.o Bmath/qlnorm.o Bmath/qlogis.o Bmath/qnbinom.o Bmath/qnchisq.o Bmath/qnorm.o Bmath/qpois.o Bmath/qt.o Bmath/qtukey.o Bmath/qunif.o Bmath/qweibull.o Bmath/rbeta.o Bmath/rbinom.o Bmath/rcauchy.o Bmath/rchisq.o Bmath/rexp.o Bmath/rf.o Bmath/rgamma.o Bmath/rgeom.o Bmath/rhyper.o Bmath/rlnorm.o Bmath/rlogis.o Bmath/rmultinom.o Bmath/rnbinom.o Bmath/rnchisq.o Bmath/rnorm.o Bmath/rpois.o Bmath/rt.o Bmath/runif.o Bmath/rweibull.o Bmath/sexp.o Bmath/sign.o Bmath/snorm.o Bmath/stirlerr.o Bmath/toms708.o Bmath/unif_rand.o Samplers/ARMS.o Samplers/DirectProposal.o Samplers/ImportanceResampler.o Samplers/MH_Proposals.o Samplers/MetropolisHastings.o Samplers/MoveAccounting.o Samplers/RejectionSampler.o Samplers/Sampler.o Samplers/ScalarAdaptiveRejectionSampler.o Samplers/ScalarLangevinSampler.o Samplers/ScalarSliceSampler.o Samplers/SliceSampler.o Samplers/TIM.o Samplers/UnivariateLangevinSampler.o Samplers/UnivariateSliceSampler.o Samplers/Gilks/arms.o stats/Bspline.o stats/ChiSquareTest.o stats/DataTable.o stats/Design.o stats/ECDF.o stats/FreqDist.o stats/IQagent.o stats/NaturalSpline.o stats/Resampler.o stats/Spline.o stats/compare_binomial_proportions.o stats/compare_predictions.o stats/diff.o stats/moments.o stats/regression.o stats/simple_random_sample.o Models/StateSpace/AggregatedStateSpaceRegression.o Models/StateSpace/StateSpaceLogitModel.o Models/StateSpace/StateSpaceModel.o Models/StateSpace/StateSpaceModelBase.o Models/StateSpace/StateSpaceNormalMixture.o Models/StateSpace/StateSpacePoissonModel.o Models/StateSpace/StateSpaceRegressionModel.o Models/StateSpace/StateSpaceStudentRegressionModel.o Models/StateSpace/Filters/KalmanTools.o Models/StateSpace/Filters/SparseKalmanTools.o Models/StateSpace/Filters/SparseMatrix.o Models/StateSpace/Filters/SparseVector.o Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.o Models/StateSpace/StateModels/ArStateModel.o Models/StateSpace/StateModels/DynamicRegressionStateModel.o Models/StateSpace/StateModels/Holiday.o Models/StateSpace/StateModels/LocalLevelStateModel.o Models/StateSpace/StateModels/LocalLinearTrend.o Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.o Models/StateSpace/StateModels/RandomWalkHolidayStateModel.o Models/StateSpace/StateModels/RegressionStateModel.o Models/StateSpace/StateModels/SeasonalStateModel.o Models/StateSpace/StateModels/StateModel.o Models/StateSpace/StateModels/StudentLocalLinearTrend.o Models/StateSpace/StateModels/TrigStateModel.o TargetFun/JacobianChecker.o TargetFun/LogPost.o TargetFun/ScalarLogpostTF.o TargetFun/TargetFun.o TargetFun/Transformation.o Models/TimeSeries/ArModel.o Models/TimeSeries/NonzeroMeanAr1Model.o Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.o Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.o Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.o cpputil/Constants.o cpputil/Date.o cpputil/DateTime.o cpputil/DefaultVnames.o cpputil/LongString.o cpputil/OutputTable.o cpputil/ParamHolder.o cpputil/Polynomial.o cpputil/Redirector.o cpputil/apply_permutation.o cpputil/cat_string.o cpputil/compare_vector_bool.o cpputil/get_date.o cpputil/gll.o cpputil/infinity.o cpputil/is_all_white.o cpputil/is_numeric.o cpputil/legalize_file_name.o cpputil/lse.o cpputil/parse_range.o cpputil/print_columns.o cpputil/read_file.o cpputil/rep.o cpputil/replace_all.o cpputil/report_error.o cpputil/safelog.o cpputil/split.o cpputil/split_delimited.o cpputil/split_string.o cpputil/str2d.o cpputil/strip.o cpputil/strip_path.o cpputil/strip_white_space.o cpputil/substring_delimited.o cpputil/trim_white_space.o
-o Boom.so Models/Bart/Bart.o Models/Bart/GaussianBartModel.o Models/Bart/GaussianLinearBartModel.o Models/Bart/LogitBartModel.o Models/Bart/PoissonBartModel.o Models/Bart/ProbitBartModel.o Models/Bart/ResidualRegressionData.o Models/Bart/PosteriorSamplers/BartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.o Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.o Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.o Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.o distributions/BinomialDistribution.o distributions/BoundedAdaptiveRejectionSampler.o distributions/DoublyBoundedAdaptiveRejectionSampler.o distributions/Markov.o distributions/Rmath_dist.o distributions/Tn2Sampler.o distributions/Wishart.o distributions/dirichlet.o distributions/extreme_value.o distributions/inverse_gaussian.o distributions/matrix_normal.o distributions/mvn.o distributions/mvt.o distributions/random_cor.o distributions/random_int.o distributions/rlexp.o distributions/rmulti.o distributions/rng.o distributions/rtriangle.o distributions/student_fix.o distributions/trun_exp.o distributions/trun_gamma.o distributions/trun_logit.o distributions/trun_norm.o distributions/usp.o Models/Glm/AggregatedRegressionModel.o Models/Glm/BinomialLogitModel.o Models/Glm/BinomialProbitModel.o Models/Glm/BinomialRegressionData.o Models/Glm/ChoiceData.o Models/Glm/CumulativeLogitModel.o Models/Glm/CumulativeProbitModel.o Models/Glm/GammaRegressionModel.o Models/Glm/Glm.o Models/Glm/GlmCoefs.o Models/Glm/HierarchicalPoissonRegression.o Models/Glm/LogisticRegressionModel.o Models/Glm/MultinomialLogitModel.o Models/Glm/MultinomialProbitModel.o Models/Glm/MvReg2.o Models/Glm/MvnGivenX.o Models/Glm/MvnGivenXandSigma.o Models/Glm/MvtRegModel.o Models/Glm/OrdinalCutpointModel.o Models/Glm/PoissonRegressionData.o Models/Glm/PoissonRegressionModel.o Models/Glm/ProbitRegression.o Models/Glm/RegressionModel.o Models/Glm/TRegression.o Models/Glm/VariableSelectionPrior.o Models/Glm/WeightedRegressionModel.o Models/Glm/ZeroInflatedGammaRegression.o Models/Glm/ZeroInflatedLognormalRegression.o Models/Glm/ZeroInflatedPoissonRegression.o Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.o Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.o Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.o Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.o Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.o Models/Glm/PosteriorSamplers/BregVsSampler.o Models/Glm/PosteriorSamplers/CumulativeLogitSampler.o Models/Glm/PosteriorSamplers/CumulativeProbitSampler.o Models/Glm/PosteriorSamplers/DAFE_MLM.o Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/LogitSampler.o Models/Glm/PosteriorSamplers/LogitSamplerBma.o Models/Glm/PosteriorSamplers/MLAuxMixSampler.o Models/Glm/PosteriorSamplers/MLVS.o Models/Glm/PosteriorSamplers/MLVS_data_imputer.o Models/Glm/PosteriorSamplers/MlogitRwm.o Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.o Models/Glm/PosteriorSamplers/MnpBetaSampler.o Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.o Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/MvRegSampler.o Models/Glm/PosteriorSamplers/MvtRegSampler.o Models/Glm/PosteriorSamplers/NormalMixtureApproximation.o Models/Glm/PosteriorSamplers/PartRegSampler.o Models/Glm/PosteriorSamplers/PoissonDataImputer.o Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/ProbitRegressionSampler.o Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/RegressionConjSampler.o Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.o Models/Glm/PosteriorSamplers/SpikeSlabSampler.o Models/Glm/PosteriorSamplers/TDataImputer.o Models/Glm/PosteriorSamplers/TRegressionSampler.o Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/VsPriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/draw_logit_lambda.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o Models/Hierarchical/HierarchicalDirichletModel.o Models/Hierarchical/HierarchicalGammaModel.o Models/Hierarchical/HierarchicalPoissonModel.o Models/Hierarchical/HierarchicalZeroInflatedGammaModel.o Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.o Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.o Models/HMM/HMM2.o Models/HMM/HealthStateModel.o Models/HMM/HmmDataImputer.o Models/HMM/HmmFilter.o Models/HMM/hmm_tools.o Models/HMM/Clickstream/Event.o Models/HMM/Clickstream/NestedHmm.o Models/HMM/Clickstream/Session.o Models/HMM/Clickstream/Stream.o Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.o Models/HMM/PosteriorSamplers/HmmPosteriorSampler.o Models/IRT/DafePcrDataImputer.o Models/IRT/DafePcrItemSampler.o Models/IRT/DafePcrRwmItemSampler.o Models/IRT/DafePcrRwmSubject.o Models/IRT/DafePcrSubject.o Models/IRT/IRT.o Models/IRT/IrtModel.o Models/IRT/Item.o Models/IRT/PartialCreditModel.o Models/IRT/Subject.o Models/IRT/SubjectPrior.o Models/IRT/SubjectSliceSampler.o LinAlg/Array.o LinAlg/Array3.o LinAlg/ArrayIterator.o LinAlg/Cholesky.o LinAlg/CorrelationMatrix.o LinAlg/DiagonalMatrix.o LinAlg/Eigen.o LinAlg/Givens.o LinAlg/Kronecker.o LinAlg/LU.o LinAlg/LinAlgExceptions.o LinAlg/Matrix.o LinAlg/MatrixPartition.o LinAlg/QR.o LinAlg/SVD.o LinAlg/SWEEP.o LinAlg/Selector.o LinAlg/SpdMatrix.o LinAlg/SubMatrix.o LinAlg/Vector.o LinAlg/VectorView.o LinAlg/blas.o LinAlg/stack_columns.o math/cephes/chbevl.o math/cephes/dawsn.o math/cephes/ei.o math/cephes/expn.o math/cephes/fac.o math/cephes/fresnl.o math/cephes/planck.o math/cephes/polevl.o math/cephes/polylog.o math/cephes/powi.o math/cephes/rgamma.o math/cephes/shichi.o math/cephes/sici.o math/cephes/spence.o math/cephes/zeta.o math/cephes/zetac.o Models/Mixtures/ConditionalFiniteMixtureModel.o Models/Mixtures/DirichletProcessMvnModel.o Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.o Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.o Models/BetaBinomialModel.o Models/BetaModel.o Models/BinomialModel.o Models/CategoricalData.o Models/ChisqModel.o Models/CompositeData.o Models/CompositeModel.o Models/CompositeVectorModel.o Models/ConstrainedVectorParams.o Models/DataTypes.o Models/DirichletModel.o Models/DiscreteUniformModel.o Models/ExponentialModel.o Models/FiniteMixtureModel.o Models/GammaModel.o Models/GaussianModel.o Models/GaussianModelBase.o Models/GaussianModelGivenSigma.o Models/IndependentMvnModel.o Models/IndependentMvnModelGivenScalarSigma.o Models/LognormalModel.o Models/MarginallyUniformCorrelationModel.o Models/MarkovModel.o Models/ModelTypes.o Models/MultinomialModel.o Models/MvnBase.o Models/MvnGivenScalarSigma.o Models/MvnGivenSigma.o Models/MvnModel.o Models/MvtModel.o Models/ParamTypes.o Models/PoissonGammaModel.o Models/PoissonModel.o Models/ProductDirichletModel.o Models/ScaledChisqModel.o Models/SpdData.o Models/SpdModel.o Models/SpdParams.o Models/Sufstat.o Models/TruncatedGammaModel.o Models/UniformCorrelationModel.o Models/UniformModel.o Models/UniformShrinkagePriorModel.o Models/WeightedGaussianSuf.o Models/WeightedMvnModel.o Models/WishartModel.o Models/ZeroInflatedGammaModel.o Models/ZeroInflatedLognormalModel.o Models/ZeroInflatedPoissonModel.o Models/ZeroMeanGaussianModel.o Models/ZeroMeanMvnModel.o Models/Policies/CompositeParamPolicy.o Models/Policies/ManyParamPolicy.o Models/Policies/MixtureDataPolicy.o Models/Policies/NullParamPolicy.o Models/Policies/PriorPolicy.o Models/PosteriorSamplers/AbsorbingMarkovConjSampler.o Models/PosteriorSamplers/BetaBinomialPosteriorSampler.o Models/PosteriorSamplers/BetaBinomialSampler.o Models/PosteriorSamplers/BetaPosteriorSampler.o Models/PosteriorSamplers/CompositeModelSampler.o Models/PosteriorSamplers/CompositeSampler.o Models/PosteriorSamplers/CorrelationSampler.o Models/PosteriorSamplers/DirichletPosteriorSampler.o Models/PosteriorSamplers/ExchangeableDirichletSampler.o Models/PosteriorSamplers/ExponentialGammaSampler.o Models/PosteriorSamplers/FixedProbBinomialSampler.o Models/PosteriorSamplers/GammaPosteriorSampler.o Models/PosteriorSamplers/GaussianConjSampler.o Models/PosteriorSamplers/GaussianMeanSampler.o Models/PosteriorSamplers/GaussianVarSampler.o Models/PosteriorSamplers/GenericGaussianVarianceSampler.o Models/PosteriorSamplers/IndependentMvnConjSampler.o Models/PosteriorSamplers/IndependentMvnVarSampler.o Models/PosteriorSamplers/MarkovConjSampler.o Models/PosteriorSamplers/MarkovConjShrinkageSampler.o Models/PosteriorSamplers/MultinomialDirichletSampler.o Models/PosteriorSamplers/MvnConjSampler.o Models/PosteriorSamplers/MvnIndependentVarianceSampler.o Models/PosteriorSamplers/MvnMeanSampler.o Models/PosteriorSamplers/MvnVarSampler.o Models/PosteriorSamplers/PoissonGammaPosteriorSampler.o Models/PosteriorSamplers/PoissonGammaSampler.o Models/PosteriorSamplers/PosteriorSampler.o Models/PosteriorSamplers/ProductDirichletPosteriorSampler.o Models/PosteriorSamplers/SepStratSampler.o Models/PosteriorSamplers/SharedSigsqSampler.o Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedPoissonSampler.o Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.o numopt/Brent.o numopt/Integral.o numopt/Negate.o numopt/NelderMead.o numopt/NumericalDerivatives.o numopt/Powell.o numopt/ScalarLaplaceApproximation.o numopt/ScalarNewtonMax.o numopt/bfgs.o numopt/conj_grad.o numopt/initialize_derivatives.o numopt/max_nd.o numopt/nelder_mead.o numopt/newton.o numopt/simulated_annealing.o Models/PointProcess/BoundedPoissonProcessSimulator.o Models/PointProcess/CosinePoissonProcess.o Models/PointProcess/HomogeneousPoissonProcess.o Models/PointProcess/MarkovModulatedPoissonProcess.o Models/PointProcess/PointProcess.o Models/PointProcess/PoissonClusterProcess.o Models/PointProcess/WeeklyCyclePoissonProcess.o Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.o boom_r_tools.o create_mixture_component.o create_point_process.o create_poisson_cluster_components.o create_poisson_process.o create_state_model.o determine_nthreads.o extract_mixture_data.o handle_exception.o list_io.o parse_model_formula.o print_R_timestamp.o prior_specification.o seed_rng_from_R.o spike_slab_prior.o Bmath/bd0.o Bmath/beta.o Bmath/chebyshev.o Bmath/choose.o Bmath/d1mach.o Bmath/dbeta.o Bmath/dbinom.o Bmath/dcauchy.o Bmath/dchisq.o Bmath/dexp.o Bmath/df.o Bmath/dgamma.o Bmath/dgeom.o Bmath/dhyper.o Bmath/dlnorm.o Bmath/dlogis.o Bmath/dnbeta.o Bmath/dnbinom.o Bmath/dnchisq.o Bmath/dnorm.o Bmath/dpois.o Bmath/dt.o Bmath/dunif.o Bmath/dweibull.o Bmath/fprec.o Bmath/fround.o Bmath/fsign.o Bmath/ftrunc.o Bmath/gamma_cody.o Bmath/gammalims.o Bmath/i1mach.o Bmath/lbeta.o Bmath/lgammacor.o Bmath/mathlib_error.o Bmath/mlutils.o Bmath/pbeta.o Bmath/pbinom.o Bmath/pcauchy.o Bmath/pchisq.o Bmath/pexp.o Bmath/pf.o Bmath/pgamma.o Bmath/pgeom.o Bmath/phyper.o Bmath/plnorm.o Bmath/plogis.o Bmath/pnbeta.o Bmath/pnbinom.o Bmath/pnchisq.o Bmath/pnf.o Bmath/pnorm.o Bmath/pnt.o Bmath/polygamma.o Bmath/ppois.o Bmath/pt.o Bmath/ptukey.o Bmath/punif.o Bmath/pweibull.o Bmath/qbeta.o Bmath/qbinom.o Bmath/qcauchy.o Bmath/qchisq.o Bmath/qexp.o Bmath/qf.o Bmath/qgamma.o Bmath/qgeom.o Bmath/qhyper.o Bmath/qlnorm.o Bmath/qlogis.o Bmath/qnbinom.o Bmath/qnchisq.o Bmath/qnorm.o Bmath/qpois.o Bmath/qt.o Bmath/qtukey.o Bmath/qunif.o Bmath/qweibull.o Bmath/rbeta.o Bmath/rbinom.o Bmath/rcauchy.o Bmath/rchisq.o Bmath/rexp.o Bmath/rf.o Bmath/rgamma.o Bmath/rgeom.o Bmath/rhyper.o Bmath/rlnorm.o Bmath/rlogis.o Bmath/rmultinom.o Bmath/rnbinom.o Bmath/rnchisq.o Bmath/rnorm.o Bmath/rpois.o Bmath/rt.o Bmath/runif.o Bmath/rweibull.o Bmath/sexp.o Bmath/sign.o Bmath/snorm.o Bmath/stirlerr.o Bmath/toms708.o Bmath/unif_rand.o Samplers/ARMS.o Samplers/DirectProposal.o Samplers/ImportanceResampler.o Samplers/MH_Proposals.o Samplers/MetropolisHastings.o Samplers/MoveAccounting.o Samplers/RejectionSampler.o Samplers/Sampler.o Samplers/ScalarAdaptiveRejectionSampler.o Samplers/ScalarLangevinSampler.o Samplers/ScalarSliceSampler.o Samplers/SliceSampler.o Samplers/TIM.o Samplers/UnivariateLangevinSampler.o Samplers/UnivariateSliceSampler.o Samplers/Gilks/arms.o stats/Bspline.o stats/ChiSquareTest.o stats/DataTable.o stats/Design.o stats/ECDF.o stats/FreqDist.o stats/IQagent.o stats/NaturalSpline.o stats/Resampler.o stats/Spline.o stats/compare_binomial_proportions.o stats/compare_predictions.o stats/diff.o stats/moments.o stats/regression.o stats/simple_random_sample.o Models/StateSpace/AggregatedStateSpaceRegression.o Models/StateSpace/StateSpaceLogitModel.o Models/StateSpace/StateSpaceModel.o Models/StateSpace/StateSpaceModelBase.o Models/StateSpace/StateSpaceNormalMixture.o Models/StateSpace/StateSpacePoissonModel.o Models/StateSpace/StateSpaceRegressionModel.o Models/StateSpace/StateSpaceStudentRegressionModel.o Models/StateSpace/Filters/KalmanTools.o Models/StateSpace/Filters/SparseKalmanTools.o Models/StateSpace/Filters/SparseMatrix.o Models/StateSpace/Filters/SparseVector.o Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.o Models/StateSpace/StateModels/ArStateModel.o Models/StateSpace/StateModels/DynamicRegressionStateModel.o Models/StateSpace/StateModels/Holiday.o Models/StateSpace/StateModels/LocalLevelStateModel.o Models/StateSpace/StateModels/LocalLinearTrend.o Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.o Models/StateSpace/StateModels/RandomWalkHolidayStateModel.o Models/StateSpace/StateModels/RegressionStateModel.o Models/StateSpace/StateModels/SeasonalStateModel.o Models/StateSpace/StateModels/StateModel.o Models/StateSpace/StateModels/StudentLocalLinearTrend.o Models/StateSpace/StateModels/TrigStateModel.o TargetFun/JacobianChecker.o TargetFun/LogPost.o TargetFun/ScalarLogpostTF.o TargetFun/TargetFun.o TargetFun/Transformation.o Models/TimeSeries/ArModel.o Models/TimeSeries/NonzeroMeanAr1Model.o Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.o Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.o Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.o cpputil/Constants.o cpputil/Date.o cpputil/DateTime.o cpputil/DefaultVnames.o cpputil/LongString.o cpputil/OutputTable.o cpputil/ParamHolder.o cpputil/Polynomial.o cpputil/Redirector.o cpputil/apply_permutation.o cpputil/cat_string.o cpputil/compare_vector_bool.o cpputil/get_date.o cpputil/gll.o cpputil/infinity.o cpputil/is_all_white.o cpputil/is_numeric.o cpputil/legalize_file_name.o cpputil/lse.o cpputil/parse_range.o cpputil/print_columns.o cpputil/read_file.o cpputil/rep.o cpputil/replace_all.o cpputil/report_error.o cpputil/safelog.o cpputil/split.o cpputil/split_delimited.o cpputil/split_string.o cpputil/str2d.o cpputil/strip.o cpputil/strip_path.o cpputil/strip_white_space.o cpputil/substring_delimited.o cpputil/trim_white_space.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/bin/bash: line 2: -o: command not found
make: *** [Boom.so] Error 127
ERROR: compilation failed for package ‘Boom’
* removing ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/Boom’

The downloaded source packages are in
	‘/tmp/RtmphL7vQx/downloaded_packages’
Warning message:
In install.packages("Boom") :
  installation of package ‘Boom’ had non-zero exit status

boom_install_a-4.log

> devtools::install("Boom")
Installing Boom
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL '/home/bearloga/source/Boom'  \
  --library='/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2'  \
  --install-tests 

* installing *source* package ‘Boom’ ...
** package ‘Boom’ successfully unpacked and MD5 sums checked
** libs
g++-4.8  -I/usr/share/R/include -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"     -std=c++11 -c Models/Bart/Bart.cpp -o Models/Bart/Bart.o
...
g++-4.8  -I/usr/share/R/include -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"     -std=c++11 -c cpputil/trim_white_space.cpp -o cpputil/trim_white_space.o
ar rc libboom.a Models/Bart/Bart.o Models/Bart/GaussianBartModel.o Models/Bart/GaussianLinearBartModel.o Models/Bart/LogitBartModel.o Models/Bart/PoissonBartModel.o Models/Bart/ProbitBartModel.o Models/Bart/ResidualRegressionData.o Models/Bart/PosteriorSamplers/BartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.o Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.o Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.o Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.o distributions/BinomialDistribution.o distributions/BoundedAdaptiveRejectionSampler.o distributions/DoublyBoundedAdaptiveRejectionSampler.o distributions/Markov.o distributions/Rmath_dist.o distributions/Tn2Sampler.o distributions/Wishart.o distributions/dirichlet.o distributions/extreme_value.o distributions/inverse_gaussian.o distributions/matrix_normal.o distributions/mvn.o distributions/mvt.o distributions/random_cor.o distributions/random_int.o distributions/rlexp.o distributions/rmulti.o distributions/rng.o distributions/rtriangle.o distributions/student_fix.o distributions/trun_exp.o distributions/trun_gamma.o distributions/trun_logit.o distributions/trun_norm.o distributions/usp.o Models/Glm/AggregatedRegressionModel.o Models/Glm/BinomialLogitModel.o Models/Glm/BinomialProbitModel.o Models/Glm/BinomialRegressionData.o Models/Glm/ChoiceData.o Models/Glm/CumulativeLogitModel.o Models/Glm/CumulativeProbitModel.o Models/Glm/GammaRegressionModel.o Models/Glm/Glm.o Models/Glm/GlmCoefs.o Models/Glm/HierarchicalPoissonRegression.o Models/Glm/LogisticRegressionModel.o Models/Glm/MultinomialLogitModel.o Models/Glm/MultinomialProbitModel.o Models/Glm/MvReg2.o Models/Glm/MvnGivenX.o Models/Glm/MvnGivenXandSigma.o Models/Glm/MvtRegModel.o Models/Glm/OrdinalCutpointModel.o Models/Glm/PoissonRegressionData.o Models/Glm/PoissonRegressionModel.o Models/Glm/ProbitRegression.o Models/Glm/RegressionModel.o Models/Glm/TRegression.o Models/Glm/VariableSelectionPrior.o Models/Glm/WeightedRegressionModel.o Models/Glm/ZeroInflatedGammaRegression.o Models/Glm/ZeroInflatedLognormalRegression.o Models/Glm/ZeroInflatedPoissonRegression.o Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.o Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.o Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.o Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.o Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.o Models/Glm/PosteriorSamplers/BregVsSampler.o Models/Glm/PosteriorSamplers/CumulativeLogitSampler.o Models/Glm/PosteriorSamplers/CumulativeProbitSampler.o Models/Glm/PosteriorSamplers/DAFE_MLM.o Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/LogitSampler.o Models/Glm/PosteriorSamplers/LogitSamplerBma.o Models/Glm/PosteriorSamplers/MLAuxMixSampler.o Models/Glm/PosteriorSamplers/MLVS.o Models/Glm/PosteriorSamplers/MLVS_data_imputer.o Models/Glm/PosteriorSamplers/MlogitRwm.o Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.o Models/Glm/PosteriorSamplers/MnpBetaSampler.o Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.o Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/MvRegSampler.o Models/Glm/PosteriorSamplers/MvtRegSampler.o Models/Glm/PosteriorSamplers/NormalMixtureApproximation.o Models/Glm/PosteriorSamplers/PartRegSampler.o Models/Glm/PosteriorSamplers/PoissonDataImputer.o Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/ProbitRegressionSampler.o Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/RegressionConjSampler.o Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.o Models/Glm/PosteriorSamplers/SpikeSlabSampler.o Models/Glm/PosteriorSamplers/TDataImputer.o Models/Glm/PosteriorSamplers/TRegressionSampler.o Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/VsPriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/draw_logit_lambda.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o Models/Hierarchical/HierarchicalDirichletModel.o Models/Hierarchical/HierarchicalGammaModel.o Models/Hierarchical/HierarchicalPoissonModel.o Models/Hierarchical/HierarchicalZeroInflatedGammaModel.o Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.o Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.o Models/HMM/HMM2.o Models/HMM/HealthStateModel.o Models/HMM/HmmDataImputer.o Models/HMM/HmmFilter.o Models/HMM/hmm_tools.o Models/HMM/Clickstream/Event.o Models/HMM/Clickstream/NestedHmm.o Models/HMM/Clickstream/Session.o Models/HMM/Clickstream/Stream.o Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.o Models/HMM/PosteriorSamplers/HmmPosteriorSampler.o Models/IRT/DafePcrDataImputer.o Models/IRT/DafePcrItemSampler.o Models/IRT/DafePcrRwmItemSampler.o Models/IRT/DafePcrRwmSubject.o Models/IRT/DafePcrSubject.o Models/IRT/IRT.o Models/IRT/IrtModel.o Models/IRT/Item.o Models/IRT/PartialCreditModel.o Models/IRT/Subject.o Models/IRT/SubjectPrior.o Models/IRT/SubjectSliceSampler.o LinAlg/Array.o LinAlg/Array3.o LinAlg/ArrayIterator.o LinAlg/Cholesky.o LinAlg/CorrelationMatrix.o LinAlg/DiagonalMatrix.o LinAlg/Eigen.o LinAlg/Givens.o LinAlg/Kronecker.o LinAlg/LU.o LinAlg/LinAlgExceptions.o LinAlg/Matrix.o LinAlg/MatrixPartition.o LinAlg/QR.o LinAlg/SVD.o LinAlg/SWEEP.o LinAlg/Selector.o LinAlg/SpdMatrix.o LinAlg/SubMatrix.o LinAlg/Vector.o LinAlg/VectorView.o LinAlg/blas.o LinAlg/stack_columns.o math/cephes/chbevl.o math/cephes/dawsn.o math/cephes/ei.o math/cephes/expn.o math/cephes/fac.o math/cephes/fresnl.o math/cephes/planck.o math/cephes/polevl.o math/cephes/polylog.o math/cephes/powi.o math/cephes/rgamma.o math/cephes/shichi.o math/cephes/sici.o math/cephes/spence.o math/cephes/zeta.o math/cephes/zetac.o Models/Mixtures/ConditionalFiniteMixtureModel.o Models/Mixtures/DirichletProcessMvnModel.o Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.o Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.o Models/BetaBinomialModel.o Models/BetaModel.o Models/BinomialModel.o Models/CategoricalData.o Models/ChisqModel.o Models/CompositeData.o Models/CompositeModel.o Models/CompositeVectorModel.o Models/ConstrainedVectorParams.o Models/DataTypes.o Models/DirichletModel.o Models/DiscreteUniformModel.o Models/ExponentialModel.o Models/FiniteMixtureModel.o Models/GammaModel.o Models/GaussianModel.o Models/GaussianModelBase.o Models/GaussianModelGivenSigma.o Models/IndependentMvnModel.o Models/IndependentMvnModelGivenScalarSigma.o Models/LognormalModel.o Models/MarginallyUniformCorrelationModel.o Models/MarkovModel.o Models/ModelTypes.o Models/MultinomialModel.o Models/MvnBase.o Models/MvnGivenScalarSigma.o Models/MvnGivenSigma.o Models/MvnModel.o Models/MvtModel.o Models/ParamTypes.o Models/PoissonGammaModel.o Models/PoissonModel.o Models/ProductDirichletModel.o Models/ScaledChisqModel.o Models/SpdData.o Models/SpdModel.o Models/SpdParams.o Models/Sufstat.o Models/TruncatedGammaModel.o Models/UniformCorrelationModel.o Models/UniformModel.o Models/UniformShrinkagePriorModel.o Models/WeightedGaussianSuf.o Models/WeightedMvnModel.o Models/WishartModel.o Models/ZeroInflatedGammaModel.o Models/ZeroInflatedLognormalModel.o Models/ZeroInflatedPoissonModel.o Models/ZeroMeanGaussianModel.o Models/ZeroMeanMvnModel.o Models/Policies/CompositeParamPolicy.o Models/Policies/ManyParamPolicy.o Models/Policies/MixtureDataPolicy.o Models/Policies/NullParamPolicy.o Models/Policies/PriorPolicy.o Models/PosteriorSamplers/AbsorbingMarkovConjSampler.o Models/PosteriorSamplers/BetaBinomialPosteriorSampler.o Models/PosteriorSamplers/BetaBinomialSampler.o Models/PosteriorSamplers/BetaPosteriorSampler.o Models/PosteriorSamplers/CompositeModelSampler.o Models/PosteriorSamplers/CompositeSampler.o Models/PosteriorSamplers/CorrelationSampler.o Models/PosteriorSamplers/DirichletPosteriorSampler.o Models/PosteriorSamplers/ExchangeableDirichletSampler.o Models/PosteriorSamplers/ExponentialGammaSampler.o Models/PosteriorSamplers/FixedProbBinomialSampler.o Models/PosteriorSamplers/GammaPosteriorSampler.o Models/PosteriorSamplers/GaussianConjSampler.o Models/PosteriorSamplers/GaussianMeanSampler.o Models/PosteriorSamplers/GaussianVarSampler.o Models/PosteriorSamplers/GenericGaussianVarianceSampler.o Models/PosteriorSamplers/IndependentMvnConjSampler.o Models/PosteriorSamplers/IndependentMvnVarSampler.o Models/PosteriorSamplers/MarkovConjSampler.o Models/PosteriorSamplers/MarkovConjShrinkageSampler.o Models/PosteriorSamplers/MultinomialDirichletSampler.o Models/PosteriorSamplers/MvnConjSampler.o Models/PosteriorSamplers/MvnIndependentVarianceSampler.o Models/PosteriorSamplers/MvnMeanSampler.o Models/PosteriorSamplers/MvnVarSampler.o Models/PosteriorSamplers/PoissonGammaPosteriorSampler.o Models/PosteriorSamplers/PoissonGammaSampler.o Models/PosteriorSamplers/PosteriorSampler.o Models/PosteriorSamplers/ProductDirichletPosteriorSampler.o Models/PosteriorSamplers/SepStratSampler.o Models/PosteriorSamplers/SharedSigsqSampler.o Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedPoissonSampler.o Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.o numopt/Brent.o numopt/Integral.o numopt/Negate.o numopt/NelderMead.o numopt/NumericalDerivatives.o numopt/Powell.o numopt/ScalarLaplaceApproximation.o numopt/ScalarNewtonMax.o numopt/bfgs.o numopt/conj_grad.o numopt/initialize_derivatives.o numopt/max_nd.o numopt/nelder_mead.o numopt/newton.o numopt/simulated_annealing.o Models/PointProcess/BoundedPoissonProcessSimulator.o Models/PointProcess/CosinePoissonProcess.o Models/PointProcess/HomogeneousPoissonProcess.o Models/PointProcess/MarkovModulatedPoissonProcess.o Models/PointProcess/PointProcess.o Models/PointProcess/PoissonClusterProcess.o Models/PointProcess/WeeklyCyclePoissonProcess.o Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.o boom_r_tools.o create_mixture_component.o create_point_process.o create_poisson_cluster_components.o create_poisson_process.o create_state_model.o determine_nthreads.o extract_mixture_data.o handle_exception.o list_io.o parse_model_formula.o print_R_timestamp.o prior_specification.o seed_rng_from_R.o spike_slab_prior.o Bmath/bd0.o Bmath/beta.o Bmath/chebyshev.o Bmath/choose.o Bmath/d1mach.o Bmath/dbeta.o Bmath/dbinom.o Bmath/dcauchy.o Bmath/dchisq.o Bmath/dexp.o Bmath/df.o Bmath/dgamma.o Bmath/dgeom.o Bmath/dhyper.o Bmath/dlnorm.o Bmath/dlogis.o Bmath/dnbeta.o Bmath/dnbinom.o Bmath/dnchisq.o Bmath/dnorm.o Bmath/dpois.o Bmath/dt.o Bmath/dunif.o Bmath/dweibull.o Bmath/fprec.o Bmath/fround.o Bmath/fsign.o Bmath/ftrunc.o Bmath/gamma_cody.o Bmath/gammalims.o Bmath/i1mach.o Bmath/lbeta.o Bmath/lgammacor.o Bmath/mathlib_error.o Bmath/mlutils.o Bmath/pbeta.o Bmath/pbinom.o Bmath/pcauchy.o Bmath/pchisq.o Bmath/pexp.o Bmath/pf.o Bmath/pgamma.o Bmath/pgeom.o Bmath/phyper.o Bmath/plnorm.o Bmath/plogis.o Bmath/pnbeta.o Bmath/pnbinom.o Bmath/pnchisq.o Bmath/pnf.o Bmath/pnorm.o Bmath/pnt.o Bmath/polygamma.o Bmath/ppois.o Bmath/pt.o Bmath/ptukey.o Bmath/punif.o Bmath/pweibull.o Bmath/qbeta.o Bmath/qbinom.o Bmath/qcauchy.o Bmath/qchisq.o Bmath/qexp.o Bmath/qf.o Bmath/qgamma.o Bmath/qgeom.o Bmath/qhyper.o Bmath/qlnorm.o Bmath/qlogis.o Bmath/qnbinom.o Bmath/qnchisq.o Bmath/qnorm.o Bmath/qpois.o Bmath/qt.o Bmath/qtukey.o Bmath/qunif.o Bmath/qweibull.o Bmath/rbeta.o Bmath/rbinom.o Bmath/rcauchy.o Bmath/rchisq.o Bmath/rexp.o Bmath/rf.o Bmath/rgamma.o Bmath/rgeom.o Bmath/rhyper.o Bmath/rlnorm.o Bmath/rlogis.o Bmath/rmultinom.o Bmath/rnbinom.o Bmath/rnchisq.o Bmath/rnorm.o Bmath/rpois.o Bmath/rt.o Bmath/runif.o Bmath/rweibull.o Bmath/sexp.o Bmath/sign.o Bmath/snorm.o Bmath/stirlerr.o Bmath/toms708.o Bmath/unif_rand.o Samplers/ARMS.o Samplers/DirectProposal.o Samplers/ImportanceResampler.o Samplers/MH_Proposals.o Samplers/MetropolisHastings.o Samplers/MoveAccounting.o Samplers/RejectionSampler.o Samplers/Sampler.o Samplers/ScalarAdaptiveRejectionSampler.o Samplers/ScalarLangevinSampler.o Samplers/ScalarSliceSampler.o Samplers/SliceSampler.o Samplers/TIM.o Samplers/UnivariateLangevinSampler.o Samplers/UnivariateSliceSampler.o Samplers/Gilks/arms.o stats/Bspline.o stats/ChiSquareTest.o stats/DataTable.o stats/Design.o stats/ECDF.o stats/FreqDist.o stats/IQagent.o stats/NaturalSpline.o stats/Resampler.o stats/Spline.o stats/compare_binomial_proportions.o stats/compare_predictions.o stats/diff.o stats/moments.o stats/regression.o stats/simple_random_sample.o Models/StateSpace/AggregatedStateSpaceRegression.o Models/StateSpace/StateSpaceLogitModel.o Models/StateSpace/StateSpaceModel.o Models/StateSpace/StateSpaceModelBase.o Models/StateSpace/StateSpaceNormalMixture.o Models/StateSpace/StateSpacePoissonModel.o Models/StateSpace/StateSpaceRegressionModel.o Models/StateSpace/StateSpaceStudentRegressionModel.o Models/StateSpace/Filters/KalmanTools.o Models/StateSpace/Filters/SparseKalmanTools.o Models/StateSpace/Filters/SparseMatrix.o Models/StateSpace/Filters/SparseVector.o Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.o Models/StateSpace/StateModels/ArStateModel.o Models/StateSpace/StateModels/DynamicRegressionStateModel.o Models/StateSpace/StateModels/Holiday.o Models/StateSpace/StateModels/LocalLevelStateModel.o Models/StateSpace/StateModels/LocalLinearTrend.o Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.o Models/StateSpace/StateModels/RandomWalkHolidayStateModel.o Models/StateSpace/StateModels/RegressionStateModel.o Models/StateSpace/StateModels/SeasonalStateModel.o Models/StateSpace/StateModels/StateModel.o Models/StateSpace/StateModels/StudentLocalLinearTrend.o Models/StateSpace/StateModels/TrigStateModel.o TargetFun/JacobianChecker.o TargetFun/LogPost.o TargetFun/ScalarLogpostTF.o TargetFun/TargetFun.o TargetFun/Transformation.o Models/TimeSeries/ArModel.o Models/TimeSeries/NonzeroMeanAr1Model.o Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.o Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.o Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.o cpputil/Constants.o cpputil/Date.o cpputil/DateTime.o cpputil/DefaultVnames.o cpputil/LongString.o cpputil/OutputTable.o cpputil/ParamHolder.o cpputil/Polynomial.o cpputil/Redirector.o cpputil/apply_permutation.o cpputil/cat_string.o cpputil/compare_vector_bool.o cpputil/get_date.o cpputil/gll.o cpputil/infinity.o cpputil/is_all_white.o cpputil/is_numeric.o cpputil/legalize_file_name.o cpputil/lse.o cpputil/parse_range.o cpputil/print_columns.o cpputil/read_file.o cpputil/rep.o cpputil/replace_all.o cpputil/report_error.o cpputil/safelog.o cpputil/split.o cpputil/split_delimited.o cpputil/split_string.o cpputil/str2d.o cpputil/strip.o cpputil/strip_path.o cpputil/strip_white_space.o cpputil/substring_delimited.o cpputil/trim_white_space.o
-o Boom.so Models/Bart/Bart.o Models/Bart/GaussianBartModel.o Models/Bart/GaussianLinearBartModel.o Models/Bart/LogitBartModel.o Models/Bart/PoissonBartModel.o Models/Bart/ProbitBartModel.o Models/Bart/ResidualRegressionData.o Models/Bart/PosteriorSamplers/BartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.o Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.o Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.o Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.o distributions/BinomialDistribution.o distributions/BoundedAdaptiveRejectionSampler.o distributions/DoublyBoundedAdaptiveRejectionSampler.o distributions/Markov.o distributions/Rmath_dist.o distributions/Tn2Sampler.o distributions/Wishart.o distributions/dirichlet.o distributions/extreme_value.o distributions/inverse_gaussian.o distributions/matrix_normal.o distributions/mvn.o distributions/mvt.o distributions/random_cor.o distributions/random_int.o distributions/rlexp.o distributions/rmulti.o distributions/rng.o distributions/rtriangle.o distributions/student_fix.o distributions/trun_exp.o distributions/trun_gamma.o distributions/trun_logit.o distributions/trun_norm.o distributions/usp.o Models/Glm/AggregatedRegressionModel.o Models/Glm/BinomialLogitModel.o Models/Glm/BinomialProbitModel.o Models/Glm/BinomialRegressionData.o Models/Glm/ChoiceData.o Models/Glm/CumulativeLogitModel.o Models/Glm/CumulativeProbitModel.o Models/Glm/GammaRegressionModel.o Models/Glm/Glm.o Models/Glm/GlmCoefs.o Models/Glm/HierarchicalPoissonRegression.o Models/Glm/LogisticRegressionModel.o Models/Glm/MultinomialLogitModel.o Models/Glm/MultinomialProbitModel.o Models/Glm/MvReg2.o Models/Glm/MvnGivenX.o Models/Glm/MvnGivenXandSigma.o Models/Glm/MvtRegModel.o Models/Glm/OrdinalCutpointModel.o Models/Glm/PoissonRegressionData.o Models/Glm/PoissonRegressionModel.o Models/Glm/ProbitRegression.o Models/Glm/RegressionModel.o Models/Glm/TRegression.o Models/Glm/VariableSelectionPrior.o Models/Glm/WeightedRegressionModel.o Models/Glm/ZeroInflatedGammaRegression.o Models/Glm/ZeroInflatedLognormalRegression.o Models/Glm/ZeroInflatedPoissonRegression.o Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.o Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.o Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.o Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.o Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.o Models/Glm/PosteriorSamplers/BregVsSampler.o Models/Glm/PosteriorSamplers/CumulativeLogitSampler.o Models/Glm/PosteriorSamplers/CumulativeProbitSampler.o Models/Glm/PosteriorSamplers/DAFE_MLM.o Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/LogitSampler.o Models/Glm/PosteriorSamplers/LogitSamplerBma.o Models/Glm/PosteriorSamplers/MLAuxMixSampler.o Models/Glm/PosteriorSamplers/MLVS.o Models/Glm/PosteriorSamplers/MLVS_data_imputer.o Models/Glm/PosteriorSamplers/MlogitRwm.o Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.o Models/Glm/PosteriorSamplers/MnpBetaSampler.o Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.o Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/MvRegSampler.o Models/Glm/PosteriorSamplers/MvtRegSampler.o Models/Glm/PosteriorSamplers/NormalMixtureApproximation.o Models/Glm/PosteriorSamplers/PartRegSampler.o Models/Glm/PosteriorSamplers/PoissonDataImputer.o Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/ProbitRegressionSampler.o Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/RegressionConjSampler.o Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.o Models/Glm/PosteriorSamplers/SpikeSlabSampler.o Models/Glm/PosteriorSamplers/TDataImputer.o Models/Glm/PosteriorSamplers/TRegressionSampler.o Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/VsPriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/draw_logit_lambda.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o Models/Hierarchical/HierarchicalDirichletModel.o Models/Hierarchical/HierarchicalGammaModel.o Models/Hierarchical/HierarchicalPoissonModel.o Models/Hierarchical/HierarchicalZeroInflatedGammaModel.o Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.o Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.o Models/HMM/HMM2.o Models/HMM/HealthStateModel.o Models/HMM/HmmDataImputer.o Models/HMM/HmmFilter.o Models/HMM/hmm_tools.o Models/HMM/Clickstream/Event.o Models/HMM/Clickstream/NestedHmm.o Models/HMM/Clickstream/Session.o Models/HMM/Clickstream/Stream.o Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.o Models/HMM/PosteriorSamplers/HmmPosteriorSampler.o Models/IRT/DafePcrDataImputer.o Models/IRT/DafePcrItemSampler.o Models/IRT/DafePcrRwmItemSampler.o Models/IRT/DafePcrRwmSubject.o Models/IRT/DafePcrSubject.o Models/IRT/IRT.o Models/IRT/IrtModel.o Models/IRT/Item.o Models/IRT/PartialCreditModel.o Models/IRT/Subject.o Models/IRT/SubjectPrior.o Models/IRT/SubjectSliceSampler.o LinAlg/Array.o LinAlg/Array3.o LinAlg/ArrayIterator.o LinAlg/Cholesky.o LinAlg/CorrelationMatrix.o LinAlg/DiagonalMatrix.o LinAlg/Eigen.o LinAlg/Givens.o LinAlg/Kronecker.o LinAlg/LU.o LinAlg/LinAlgExceptions.o LinAlg/Matrix.o LinAlg/MatrixPartition.o LinAlg/QR.o LinAlg/SVD.o LinAlg/SWEEP.o LinAlg/Selector.o LinAlg/SpdMatrix.o LinAlg/SubMatrix.o LinAlg/Vector.o LinAlg/VectorView.o LinAlg/blas.o LinAlg/stack_columns.o math/cephes/chbevl.o math/cephes/dawsn.o math/cephes/ei.o math/cephes/expn.o math/cephes/fac.o math/cephes/fresnl.o math/cephes/planck.o math/cephes/polevl.o math/cephes/polylog.o math/cephes/powi.o math/cephes/rgamma.o math/cephes/shichi.o math/cephes/sici.o math/cephes/spence.o math/cephes/zeta.o math/cephes/zetac.o Models/Mixtures/ConditionalFiniteMixtureModel.o Models/Mixtures/DirichletProcessMvnModel.o Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.o Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.o Models/BetaBinomialModel.o Models/BetaModel.o Models/BinomialModel.o Models/CategoricalData.o Models/ChisqModel.o Models/CompositeData.o Models/CompositeModel.o Models/CompositeVectorModel.o Models/ConstrainedVectorParams.o Models/DataTypes.o Models/DirichletModel.o Models/DiscreteUniformModel.o Models/ExponentialModel.o Models/FiniteMixtureModel.o Models/GammaModel.o Models/GaussianModel.o Models/GaussianModelBase.o Models/GaussianModelGivenSigma.o Models/IndependentMvnModel.o Models/IndependentMvnModelGivenScalarSigma.o Models/LognormalModel.o Models/MarginallyUniformCorrelationModel.o Models/MarkovModel.o Models/ModelTypes.o Models/MultinomialModel.o Models/MvnBase.o Models/MvnGivenScalarSigma.o Models/MvnGivenSigma.o Models/MvnModel.o Models/MvtModel.o Models/ParamTypes.o Models/PoissonGammaModel.o Models/PoissonModel.o Models/ProductDirichletModel.o Models/ScaledChisqModel.o Models/SpdData.o Models/SpdModel.o Models/SpdParams.o Models/Sufstat.o Models/TruncatedGammaModel.o Models/UniformCorrelationModel.o Models/UniformModel.o Models/UniformShrinkagePriorModel.o Models/WeightedGaussianSuf.o Models/WeightedMvnModel.o Models/WishartModel.o Models/ZeroInflatedGammaModel.o Models/ZeroInflatedLognormalModel.o Models/ZeroInflatedPoissonModel.o Models/ZeroMeanGaussianModel.o Models/ZeroMeanMvnModel.o Models/Policies/CompositeParamPolicy.o Models/Policies/ManyParamPolicy.o Models/Policies/MixtureDataPolicy.o Models/Policies/NullParamPolicy.o Models/Policies/PriorPolicy.o Models/PosteriorSamplers/AbsorbingMarkovConjSampler.o Models/PosteriorSamplers/BetaBinomialPosteriorSampler.o Models/PosteriorSamplers/BetaBinomialSampler.o Models/PosteriorSamplers/BetaPosteriorSampler.o Models/PosteriorSamplers/CompositeModelSampler.o Models/PosteriorSamplers/CompositeSampler.o Models/PosteriorSamplers/CorrelationSampler.o Models/PosteriorSamplers/DirichletPosteriorSampler.o Models/PosteriorSamplers/ExchangeableDirichletSampler.o Models/PosteriorSamplers/ExponentialGammaSampler.o Models/PosteriorSamplers/FixedProbBinomialSampler.o Models/PosteriorSamplers/GammaPosteriorSampler.o Models/PosteriorSamplers/GaussianConjSampler.o Models/PosteriorSamplers/GaussianMeanSampler.o Models/PosteriorSamplers/GaussianVarSampler.o Models/PosteriorSamplers/GenericGaussianVarianceSampler.o Models/PosteriorSamplers/IndependentMvnConjSampler.o Models/PosteriorSamplers/IndependentMvnVarSampler.o Models/PosteriorSamplers/MarkovConjSampler.o Models/PosteriorSamplers/MarkovConjShrinkageSampler.o Models/PosteriorSamplers/MultinomialDirichletSampler.o Models/PosteriorSamplers/MvnConjSampler.o Models/PosteriorSamplers/MvnIndependentVarianceSampler.o Models/PosteriorSamplers/MvnMeanSampler.o Models/PosteriorSamplers/MvnVarSampler.o Models/PosteriorSamplers/PoissonGammaPosteriorSampler.o Models/PosteriorSamplers/PoissonGammaSampler.o Models/PosteriorSamplers/PosteriorSampler.o Models/PosteriorSamplers/ProductDirichletPosteriorSampler.o Models/PosteriorSamplers/SepStratSampler.o Models/PosteriorSamplers/SharedSigsqSampler.o Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedPoissonSampler.o Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.o numopt/Brent.o numopt/Integral.o numopt/Negate.o numopt/NelderMead.o numopt/NumericalDerivatives.o numopt/Powell.o numopt/ScalarLaplaceApproximation.o numopt/ScalarNewtonMax.o numopt/bfgs.o numopt/conj_grad.o numopt/initialize_derivatives.o numopt/max_nd.o numopt/nelder_mead.o numopt/newton.o numopt/simulated_annealing.o Models/PointProcess/BoundedPoissonProcessSimulator.o Models/PointProcess/CosinePoissonProcess.o Models/PointProcess/HomogeneousPoissonProcess.o Models/PointProcess/MarkovModulatedPoissonProcess.o Models/PointProcess/PointProcess.o Models/PointProcess/PoissonClusterProcess.o Models/PointProcess/WeeklyCyclePoissonProcess.o Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.o boom_r_tools.o create_mixture_component.o create_point_process.o create_poisson_cluster_components.o create_poisson_process.o create_state_model.o determine_nthreads.o extract_mixture_data.o handle_exception.o list_io.o parse_model_formula.o print_R_timestamp.o prior_specification.o seed_rng_from_R.o spike_slab_prior.o Bmath/bd0.o Bmath/beta.o Bmath/chebyshev.o Bmath/choose.o Bmath/d1mach.o Bmath/dbeta.o Bmath/dbinom.o Bmath/dcauchy.o Bmath/dchisq.o Bmath/dexp.o Bmath/df.o Bmath/dgamma.o Bmath/dgeom.o Bmath/dhyper.o Bmath/dlnorm.o Bmath/dlogis.o Bmath/dnbeta.o Bmath/dnbinom.o Bmath/dnchisq.o Bmath/dnorm.o Bmath/dpois.o Bmath/dt.o Bmath/dunif.o Bmath/dweibull.o Bmath/fprec.o Bmath/fround.o Bmath/fsign.o Bmath/ftrunc.o Bmath/gamma_cody.o Bmath/gammalims.o Bmath/i1mach.o Bmath/lbeta.o Bmath/lgammacor.o Bmath/mathlib_error.o Bmath/mlutils.o Bmath/pbeta.o Bmath/pbinom.o Bmath/pcauchy.o Bmath/pchisq.o Bmath/pexp.o Bmath/pf.o Bmath/pgamma.o Bmath/pgeom.o Bmath/phyper.o Bmath/plnorm.o Bmath/plogis.o Bmath/pnbeta.o Bmath/pnbinom.o Bmath/pnchisq.o Bmath/pnf.o Bmath/pnorm.o Bmath/pnt.o Bmath/polygamma.o Bmath/ppois.o Bmath/pt.o Bmath/ptukey.o Bmath/punif.o Bmath/pweibull.o Bmath/qbeta.o Bmath/qbinom.o Bmath/qcauchy.o Bmath/qchisq.o Bmath/qexp.o Bmath/qf.o Bmath/qgamma.o Bmath/qgeom.o Bmath/qhyper.o Bmath/qlnorm.o Bmath/qlogis.o Bmath/qnbinom.o Bmath/qnchisq.o Bmath/qnorm.o Bmath/qpois.o Bmath/qt.o Bmath/qtukey.o Bmath/qunif.o Bmath/qweibull.o Bmath/rbeta.o Bmath/rbinom.o Bmath/rcauchy.o Bmath/rchisq.o Bmath/rexp.o Bmath/rf.o Bmath/rgamma.o Bmath/rgeom.o Bmath/rhyper.o Bmath/rlnorm.o Bmath/rlogis.o Bmath/rmultinom.o Bmath/rnbinom.o Bmath/rnchisq.o Bmath/rnorm.o Bmath/rpois.o Bmath/rt.o Bmath/runif.o Bmath/rweibull.o Bmath/sexp.o Bmath/sign.o Bmath/snorm.o Bmath/stirlerr.o Bmath/toms708.o Bmath/unif_rand.o Samplers/ARMS.o Samplers/DirectProposal.o Samplers/ImportanceResampler.o Samplers/MH_Proposals.o Samplers/MetropolisHastings.o Samplers/MoveAccounting.o Samplers/RejectionSampler.o Samplers/Sampler.o Samplers/ScalarAdaptiveRejectionSampler.o Samplers/ScalarLangevinSampler.o Samplers/ScalarSliceSampler.o Samplers/SliceSampler.o Samplers/TIM.o Samplers/UnivariateLangevinSampler.o Samplers/UnivariateSliceSampler.o Samplers/Gilks/arms.o stats/Bspline.o stats/ChiSquareTest.o stats/DataTable.o stats/Design.o stats/ECDF.o stats/FreqDist.o stats/IQagent.o stats/NaturalSpline.o stats/Resampler.o stats/Spline.o stats/compare_binomial_proportions.o stats/compare_predictions.o stats/diff.o stats/moments.o stats/regression.o stats/simple_random_sample.o Models/StateSpace/AggregatedStateSpaceRegression.o Models/StateSpace/StateSpaceLogitModel.o Models/StateSpace/StateSpaceModel.o Models/StateSpace/StateSpaceModelBase.o Models/StateSpace/StateSpaceNormalMixture.o Models/StateSpace/StateSpacePoissonModel.o Models/StateSpace/StateSpaceRegressionModel.o Models/StateSpace/StateSpaceStudentRegressionModel.o Models/StateSpace/Filters/KalmanTools.o Models/StateSpace/Filters/SparseKalmanTools.o Models/StateSpace/Filters/SparseMatrix.o Models/StateSpace/Filters/SparseVector.o Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.o Models/StateSpace/StateModels/ArStateModel.o Models/StateSpace/StateModels/DynamicRegressionStateModel.o Models/StateSpace/StateModels/Holiday.o Models/StateSpace/StateModels/LocalLevelStateModel.o Models/StateSpace/StateModels/LocalLinearTrend.o Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.o Models/StateSpace/StateModels/RandomWalkHolidayStateModel.o Models/StateSpace/StateModels/RegressionStateModel.o Models/StateSpace/StateModels/SeasonalStateModel.o Models/StateSpace/StateModels/StateModel.o Models/StateSpace/StateModels/StudentLocalLinearTrend.o Models/StateSpace/StateModels/TrigStateModel.o TargetFun/JacobianChecker.o TargetFun/LogPost.o TargetFun/ScalarLogpostTF.o TargetFun/TargetFun.o TargetFun/Transformation.o Models/TimeSeries/ArModel.o Models/TimeSeries/NonzeroMeanAr1Model.o Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.o Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.o Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.o cpputil/Constants.o cpputil/Date.o cpputil/DateTime.o cpputil/DefaultVnames.o cpputil/LongString.o cpputil/OutputTable.o cpputil/ParamHolder.o cpputil/Polynomial.o cpputil/Redirector.o cpputil/apply_permutation.o cpputil/cat_string.o cpputil/compare_vector_bool.o cpputil/get_date.o cpputil/gll.o cpputil/infinity.o cpputil/is_all_white.o cpputil/is_numeric.o cpputil/legalize_file_name.o cpputil/lse.o cpputil/parse_range.o cpputil/print_columns.o cpputil/read_file.o cpputil/rep.o cpputil/replace_all.o cpputil/report_error.o cpputil/safelog.o cpputil/split.o cpputil/split_delimited.o cpputil/split_string.o cpputil/str2d.o cpputil/strip.o cpputil/strip_path.o cpputil/strip_white_space.o cpputil/substring_delimited.o cpputil/trim_white_space.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/bin/bash: line 2: -o: command not found
make: *** [Boom.so] Error 127
ERROR: compilation failed for package ‘Boom’
* removing ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/Boom’
Error: Command failed (1)

> head(readLines("Boom/src/Makevars"), 10) # proof
 [1] "all: $(SHLIB)"                                                    
 [2] "$(SHLIB): libboom.a"                                              
 [3] ""                                                                 
 [4] "CXX=g++-4.8"                                                      
 [5] "CXX1X=g++-4.8"                                                    
 [6] "CXX_STD = CXX11"                                                  
 [7] "CXX1XFLAGS=-std=c++11"                                            
 [8] ""                                                                 
 [9] "# When compiling remotely (e.g. on CRAN's winbuilder) flags to be"
[10] "# passed to make can be specified here."                          

boom_install_b.log

Installing package into ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/Boom_0.5.tar.gz'
Content type 'application/x-gzip' length 1061942 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘Boom’ ...
** package ‘Boom’ successfully unpacked and MD5 sums checked
** libs
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Models/Bart/Bart.cpp -o Models/Bart/Bart.o
...
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.cpp -o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o
Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.cpp: In function ‘void BOOM::fill_poisson_mixture_approximation_table_2(BOOM::NormalMixtureApproximationTable*)’:
Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.cpp:7:8: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
   void fill_poisson_mixture_approximation_table_2(
        ^
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.cpp -o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o
Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.cpp: In function ‘void BOOM::fill_poisson_mixture_approximation_table_3(BOOM::NormalMixtureApproximationTable*)’:
Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.cpp:7:8: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
   void fill_poisson_mixture_approximation_table_3(
        ^
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.cpp -o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o
...
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE  -I"/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/BH/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cpputil/trim_white_space.cpp -o cpputil/trim_white_space.o
ar rc libboom.a Models/Bart/Bart.o Models/Bart/GaussianBartModel.o Models/Bart/GaussianLinearBartModel.o Models/Bart/LogitBartModel.o Models/Bart/PoissonBartModel.o Models/Bart/ProbitBartModel.o Models/Bart/ResidualRegressionData.o Models/Bart/PosteriorSamplers/BartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.o Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.o Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.o Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.o distributions/BinomialDistribution.o distributions/BoundedAdaptiveRejectionSampler.o distributions/DoublyBoundedAdaptiveRejectionSampler.o distributions/Markov.o distributions/Rmath_dist.o distributions/Tn2Sampler.o distributions/Wishart.o distributions/dirichlet.o distributions/extreme_value.o distributions/inverse_gaussian.o distributions/matrix_normal.o distributions/mvn.o distributions/mvt.o distributions/random_cor.o distributions/random_int.o distributions/rlexp.o distributions/rmulti.o distributions/rng.o distributions/rtriangle.o distributions/student_fix.o distributions/trun_exp.o distributions/trun_gamma.o distributions/trun_logit.o distributions/trun_norm.o distributions/usp.o Models/Glm/AggregatedRegressionModel.o Models/Glm/BinomialLogitModel.o Models/Glm/BinomialProbitModel.o Models/Glm/BinomialRegressionData.o Models/Glm/ChoiceData.o Models/Glm/CumulativeLogitModel.o Models/Glm/CumulativeProbitModel.o Models/Glm/GammaRegressionModel.o Models/Glm/Glm.o Models/Glm/GlmCoefs.o Models/Glm/HierarchicalPoissonRegression.o Models/Glm/LogisticRegressionModel.o Models/Glm/MultinomialLogitModel.o Models/Glm/MultinomialProbitModel.o Models/Glm/MvReg2.o Models/Glm/MvnGivenX.o Models/Glm/MvnGivenXandSigma.o Models/Glm/MvtRegModel.o Models/Glm/OrdinalCutpointModel.o Models/Glm/PoissonRegressionData.o Models/Glm/PoissonRegressionModel.o Models/Glm/ProbitRegression.o Models/Glm/RegressionModel.o Models/Glm/TRegression.o Models/Glm/VariableSelectionPrior.o Models/Glm/WeightedRegressionModel.o Models/Glm/ZeroInflatedGammaRegression.o Models/Glm/ZeroInflatedLognormalRegression.o Models/Glm/ZeroInflatedPoissonRegression.o Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.o Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.o Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.o Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.o Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.o Models/Glm/PosteriorSamplers/BregVsSampler.o Models/Glm/PosteriorSamplers/CumulativeLogitSampler.o Models/Glm/PosteriorSamplers/CumulativeProbitSampler.o Models/Glm/PosteriorSamplers/DAFE_MLM.o Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/LogitSampler.o Models/Glm/PosteriorSamplers/LogitSamplerBma.o Models/Glm/PosteriorSamplers/MLAuxMixSampler.o Models/Glm/PosteriorSamplers/MLVS.o Models/Glm/PosteriorSamplers/MLVS_data_imputer.o Models/Glm/PosteriorSamplers/MlogitRwm.o Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.o Models/Glm/PosteriorSamplers/MnpBetaSampler.o Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.o Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/MvRegSampler.o Models/Glm/PosteriorSamplers/MvtRegSampler.o Models/Glm/PosteriorSamplers/NormalMixtureApproximation.o Models/Glm/PosteriorSamplers/PartRegSampler.o Models/Glm/PosteriorSamplers/PoissonDataImputer.o Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/ProbitRegressionSampler.o Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/RegressionConjSampler.o Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.o Models/Glm/PosteriorSamplers/SpikeSlabSampler.o Models/Glm/PosteriorSamplers/TDataImputer.o Models/Glm/PosteriorSamplers/TRegressionSampler.o Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/VsPriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/draw_logit_lambda.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o Models/Hierarchical/HierarchicalDirichletModel.o Models/Hierarchical/HierarchicalGammaModel.o Models/Hierarchical/HierarchicalPoissonModel.o Models/Hierarchical/HierarchicalZeroInflatedGammaModel.o Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.o Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.o Models/HMM/HMM2.o Models/HMM/HealthStateModel.o Models/HMM/HmmDataImputer.o Models/HMM/HmmFilter.o Models/HMM/hmm_tools.o Models/HMM/Clickstream/Event.o Models/HMM/Clickstream/NestedHmm.o Models/HMM/Clickstream/Session.o Models/HMM/Clickstream/Stream.o Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.o Models/HMM/PosteriorSamplers/HmmPosteriorSampler.o Models/IRT/DafePcrDataImputer.o Models/IRT/DafePcrItemSampler.o Models/IRT/DafePcrRwmItemSampler.o Models/IRT/DafePcrRwmSubject.o Models/IRT/DafePcrSubject.o Models/IRT/IRT.o Models/IRT/IrtModel.o Models/IRT/Item.o Models/IRT/PartialCreditModel.o Models/IRT/Subject.o Models/IRT/SubjectPrior.o Models/IRT/SubjectSliceSampler.o LinAlg/Array.o LinAlg/Array3.o LinAlg/ArrayIterator.o LinAlg/Cholesky.o LinAlg/CorrelationMatrix.o LinAlg/DiagonalMatrix.o LinAlg/Eigen.o LinAlg/Givens.o LinAlg/Kronecker.o LinAlg/LU.o LinAlg/LinAlgExceptions.o LinAlg/Matrix.o LinAlg/MatrixPartition.o LinAlg/QR.o LinAlg/SVD.o LinAlg/SWEEP.o LinAlg/Selector.o LinAlg/SpdMatrix.o LinAlg/SubMatrix.o LinAlg/Vector.o LinAlg/VectorView.o LinAlg/blas.o LinAlg/stack_columns.o math/cephes/chbevl.o math/cephes/dawsn.o math/cephes/ei.o math/cephes/expn.o math/cephes/fac.o math/cephes/fresnl.o math/cephes/planck.o math/cephes/polevl.o math/cephes/polylog.o math/cephes/powi.o math/cephes/rgamma.o math/cephes/shichi.o math/cephes/sici.o math/cephes/spence.o math/cephes/zeta.o math/cephes/zetac.o Models/Mixtures/ConditionalFiniteMixtureModel.o Models/Mixtures/DirichletProcessMvnModel.o Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.o Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.o Models/BetaBinomialModel.o Models/BetaModel.o Models/BinomialModel.o Models/CategoricalData.o Models/ChisqModel.o Models/CompositeData.o Models/CompositeModel.o Models/CompositeVectorModel.o Models/ConstrainedVectorParams.o Models/DataTypes.o Models/DirichletModel.o Models/DiscreteUniformModel.o Models/ExponentialModel.o Models/FiniteMixtureModel.o Models/GammaModel.o Models/GaussianModel.o Models/GaussianModelBase.o Models/GaussianModelGivenSigma.o Models/IndependentMvnModel.o Models/IndependentMvnModelGivenScalarSigma.o Models/LognormalModel.o Models/MarginallyUniformCorrelationModel.o Models/MarkovModel.o Models/ModelTypes.o Models/MultinomialModel.o Models/MvnBase.o Models/MvnGivenScalarSigma.o Models/MvnGivenSigma.o Models/MvnModel.o Models/MvtModel.o Models/ParamTypes.o Models/PoissonGammaModel.o Models/PoissonModel.o Models/ProductDirichletModel.o Models/ScaledChisqModel.o Models/SpdData.o Models/SpdModel.o Models/SpdParams.o Models/Sufstat.o Models/TruncatedGammaModel.o Models/UniformCorrelationModel.o Models/UniformModel.o Models/UniformShrinkagePriorModel.o Models/WeightedGaussianSuf.o Models/WeightedMvnModel.o Models/WishartModel.o Models/ZeroInflatedGammaModel.o Models/ZeroInflatedLognormalModel.o Models/ZeroInflatedPoissonModel.o Models/ZeroMeanGaussianModel.o Models/ZeroMeanMvnModel.o Models/Policies/CompositeParamPolicy.o Models/Policies/ManyParamPolicy.o Models/Policies/MixtureDataPolicy.o Models/Policies/NullParamPolicy.o Models/Policies/PriorPolicy.o Models/PosteriorSamplers/AbsorbingMarkovConjSampler.o Models/PosteriorSamplers/BetaBinomialPosteriorSampler.o Models/PosteriorSamplers/BetaBinomialSampler.o Models/PosteriorSamplers/BetaPosteriorSampler.o Models/PosteriorSamplers/CompositeModelSampler.o Models/PosteriorSamplers/CompositeSampler.o Models/PosteriorSamplers/CorrelationSampler.o Models/PosteriorSamplers/DirichletPosteriorSampler.o Models/PosteriorSamplers/ExchangeableDirichletSampler.o Models/PosteriorSamplers/ExponentialGammaSampler.o Models/PosteriorSamplers/FixedProbBinomialSampler.o Models/PosteriorSamplers/GammaPosteriorSampler.o Models/PosteriorSamplers/GaussianConjSampler.o Models/PosteriorSamplers/GaussianMeanSampler.o Models/PosteriorSamplers/GaussianVarSampler.o Models/PosteriorSamplers/GenericGaussianVarianceSampler.o Models/PosteriorSamplers/IndependentMvnConjSampler.o Models/PosteriorSamplers/IndependentMvnVarSampler.o Models/PosteriorSamplers/MarkovConjSampler.o Models/PosteriorSamplers/MarkovConjShrinkageSampler.o Models/PosteriorSamplers/MultinomialDirichletSampler.o Models/PosteriorSamplers/MvnConjSampler.o Models/PosteriorSamplers/MvnIndependentVarianceSampler.o Models/PosteriorSamplers/MvnMeanSampler.o Models/PosteriorSamplers/MvnVarSampler.o Models/PosteriorSamplers/PoissonGammaPosteriorSampler.o Models/PosteriorSamplers/PoissonGammaSampler.o Models/PosteriorSamplers/PosteriorSampler.o Models/PosteriorSamplers/ProductDirichletPosteriorSampler.o Models/PosteriorSamplers/SepStratSampler.o Models/PosteriorSamplers/SharedSigsqSampler.o Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedPoissonSampler.o Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.o numopt/Brent.o numopt/Integral.o numopt/Negate.o numopt/NelderMead.o numopt/NumericalDerivatives.o numopt/Powell.o numopt/ScalarLaplaceApproximation.o numopt/ScalarNewtonMax.o numopt/bfgs.o numopt/conj_grad.o numopt/initialize_derivatives.o numopt/max_nd.o numopt/nelder_mead.o numopt/newton.o numopt/simulated_annealing.o Models/PointProcess/BoundedPoissonProcessSimulator.o Models/PointProcess/CosinePoissonProcess.o Models/PointProcess/HomogeneousPoissonProcess.o Models/PointProcess/MarkovModulatedPoissonProcess.o Models/PointProcess/PointProcess.o Models/PointProcess/PoissonClusterProcess.o Models/PointProcess/WeeklyCyclePoissonProcess.o Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.o boom_r_tools.o create_mixture_component.o create_point_process.o create_poisson_cluster_components.o create_poisson_process.o create_state_model.o determine_nthreads.o extract_mixture_data.o handle_exception.o list_io.o parse_model_formula.o print_R_timestamp.o prior_specification.o seed_rng_from_R.o spike_slab_prior.o Bmath/bd0.o Bmath/beta.o Bmath/chebyshev.o Bmath/choose.o Bmath/d1mach.o Bmath/dbeta.o Bmath/dbinom.o Bmath/dcauchy.o Bmath/dchisq.o Bmath/dexp.o Bmath/df.o Bmath/dgamma.o Bmath/dgeom.o Bmath/dhyper.o Bmath/dlnorm.o Bmath/dlogis.o Bmath/dnbeta.o Bmath/dnbinom.o Bmath/dnchisq.o Bmath/dnorm.o Bmath/dpois.o Bmath/dt.o Bmath/dunif.o Bmath/dweibull.o Bmath/fprec.o Bmath/fround.o Bmath/fsign.o Bmath/ftrunc.o Bmath/gamma_cody.o Bmath/gammalims.o Bmath/i1mach.o Bmath/lbeta.o Bmath/lgammacor.o Bmath/mathlib_error.o Bmath/mlutils.o Bmath/pbeta.o Bmath/pbinom.o Bmath/pcauchy.o Bmath/pchisq.o Bmath/pexp.o Bmath/pf.o Bmath/pgamma.o Bmath/pgeom.o Bmath/phyper.o Bmath/plnorm.o Bmath/plogis.o Bmath/pnbeta.o Bmath/pnbinom.o Bmath/pnchisq.o Bmath/pnf.o Bmath/pnorm.o Bmath/pnt.o Bmath/polygamma.o Bmath/ppois.o Bmath/pt.o Bmath/ptukey.o Bmath/punif.o Bmath/pweibull.o Bmath/qbeta.o Bmath/qbinom.o Bmath/qcauchy.o Bmath/qchisq.o Bmath/qexp.o Bmath/qf.o Bmath/qgamma.o Bmath/qgeom.o Bmath/qhyper.o Bmath/qlnorm.o Bmath/qlogis.o Bmath/qnbinom.o Bmath/qnchisq.o Bmath/qnorm.o Bmath/qpois.o Bmath/qt.o Bmath/qtukey.o Bmath/qunif.o Bmath/qweibull.o Bmath/rbeta.o Bmath/rbinom.o Bmath/rcauchy.o Bmath/rchisq.o Bmath/rexp.o Bmath/rf.o Bmath/rgamma.o Bmath/rgeom.o Bmath/rhyper.o Bmath/rlnorm.o Bmath/rlogis.o Bmath/rmultinom.o Bmath/rnbinom.o Bmath/rnchisq.o Bmath/rnorm.o Bmath/rpois.o Bmath/rt.o Bmath/runif.o Bmath/rweibull.o Bmath/sexp.o Bmath/sign.o Bmath/snorm.o Bmath/stirlerr.o Bmath/toms708.o Bmath/unif_rand.o Samplers/ARMS.o Samplers/DirectProposal.o Samplers/ImportanceResampler.o Samplers/MH_Proposals.o Samplers/MetropolisHastings.o Samplers/MoveAccounting.o Samplers/RejectionSampler.o Samplers/Sampler.o Samplers/ScalarAdaptiveRejectionSampler.o Samplers/ScalarLangevinSampler.o Samplers/ScalarSliceSampler.o Samplers/SliceSampler.o Samplers/TIM.o Samplers/UnivariateLangevinSampler.o Samplers/UnivariateSliceSampler.o Samplers/Gilks/arms.o stats/Bspline.o stats/ChiSquareTest.o stats/DataTable.o stats/Design.o stats/ECDF.o stats/FreqDist.o stats/IQagent.o stats/NaturalSpline.o stats/Resampler.o stats/Spline.o stats/compare_binomial_proportions.o stats/compare_predictions.o stats/diff.o stats/moments.o stats/regression.o stats/simple_random_sample.o Models/StateSpace/AggregatedStateSpaceRegression.o Models/StateSpace/StateSpaceLogitModel.o Models/StateSpace/StateSpaceModel.o Models/StateSpace/StateSpaceModelBase.o Models/StateSpace/StateSpaceNormalMixture.o Models/StateSpace/StateSpacePoissonModel.o Models/StateSpace/StateSpaceRegressionModel.o Models/StateSpace/StateSpaceStudentRegressionModel.o Models/StateSpace/Filters/KalmanTools.o Models/StateSpace/Filters/SparseKalmanTools.o Models/StateSpace/Filters/SparseMatrix.o Models/StateSpace/Filters/SparseVector.o Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.o Models/StateSpace/StateModels/ArStateModel.o Models/StateSpace/StateModels/DynamicRegressionStateModel.o Models/StateSpace/StateModels/Holiday.o Models/StateSpace/StateModels/LocalLevelStateModel.o Models/StateSpace/StateModels/LocalLinearTrend.o Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.o Models/StateSpace/StateModels/RandomWalkHolidayStateModel.o Models/StateSpace/StateModels/RegressionStateModel.o Models/StateSpace/StateModels/SeasonalStateModel.o Models/StateSpace/StateModels/StateModel.o Models/StateSpace/StateModels/StudentLocalLinearTrend.o Models/StateSpace/StateModels/TrigStateModel.o TargetFun/JacobianChecker.o TargetFun/LogPost.o TargetFun/ScalarLogpostTF.o TargetFun/TargetFun.o TargetFun/Transformation.o Models/TimeSeries/ArModel.o Models/TimeSeries/NonzeroMeanAr1Model.o Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.o Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.o Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.o cpputil/Constants.o cpputil/Date.o cpputil/DateTime.o cpputil/DefaultVnames.o cpputil/LongString.o cpputil/OutputTable.o cpputil/ParamHolder.o cpputil/Polynomial.o cpputil/Redirector.o cpputil/apply_permutation.o cpputil/cat_string.o cpputil/compare_vector_bool.o cpputil/get_date.o cpputil/gll.o cpputil/infinity.o cpputil/is_all_white.o cpputil/is_numeric.o cpputil/legalize_file_name.o cpputil/lse.o cpputil/parse_range.o cpputil/print_columns.o cpputil/read_file.o cpputil/rep.o cpputil/replace_all.o cpputil/report_error.o cpputil/safelog.o cpputil/split.o cpputil/split_delimited.o cpputil/split_string.o cpputil/str2d.o cpputil/strip.o cpputil/strip_path.o cpputil/strip_white_space.o cpputil/substring_delimited.o cpputil/trim_white_space.o
g++ -std=c++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Boom.so Models/Bart/Bart.o Models/Bart/GaussianBartModel.o Models/Bart/GaussianLinearBartModel.o Models/Bart/LogitBartModel.o Models/Bart/PoissonBartModel.o Models/Bart/ProbitBartModel.o Models/Bart/ResidualRegressionData.o Models/Bart/PosteriorSamplers/BartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.o Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.o Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.o Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.o Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.o distributions/BinomialDistribution.o distributions/BoundedAdaptiveRejectionSampler.o distributions/DoublyBoundedAdaptiveRejectionSampler.o distributions/Markov.o distributions/Rmath_dist.o distributions/Tn2Sampler.o distributions/Wishart.o distributions/dirichlet.o distributions/extreme_value.o distributions/inverse_gaussian.o distributions/matrix_normal.o distributions/mvn.o distributions/mvt.o distributions/random_cor.o distributions/random_int.o distributions/rlexp.o distributions/rmulti.o distributions/rng.o distributions/rtriangle.o distributions/student_fix.o distributions/trun_exp.o distributions/trun_gamma.o distributions/trun_logit.o distributions/trun_norm.o distributions/usp.o Models/Glm/AggregatedRegressionModel.o Models/Glm/BinomialLogitModel.o Models/Glm/BinomialProbitModel.o Models/Glm/BinomialRegressionData.o Models/Glm/ChoiceData.o Models/Glm/CumulativeLogitModel.o Models/Glm/CumulativeProbitModel.o Models/Glm/GammaRegressionModel.o Models/Glm/Glm.o Models/Glm/GlmCoefs.o Models/Glm/HierarchicalPoissonRegression.o Models/Glm/LogisticRegressionModel.o Models/Glm/MultinomialLogitModel.o Models/Glm/MultinomialProbitModel.o Models/Glm/MvReg2.o Models/Glm/MvnGivenX.o Models/Glm/MvnGivenXandSigma.o Models/Glm/MvtRegModel.o Models/Glm/OrdinalCutpointModel.o Models/Glm/PoissonRegressionData.o Models/Glm/PoissonRegressionModel.o Models/Glm/ProbitRegression.o Models/Glm/RegressionModel.o Models/Glm/TRegression.o Models/Glm/VariableSelectionPrior.o Models/Glm/WeightedRegressionModel.o Models/Glm/ZeroInflatedGammaRegression.o Models/Glm/ZeroInflatedLognormalRegression.o Models/Glm/ZeroInflatedPoissonRegression.o Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.o Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.o Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.o Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.o Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.o Models/Glm/PosteriorSamplers/BinomialProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.o Models/Glm/PosteriorSamplers/BregVsSampler.o Models/Glm/PosteriorSamplers/CumulativeLogitSampler.o Models/Glm/PosteriorSamplers/CumulativeProbitSampler.o Models/Glm/PosteriorSamplers/DAFE_MLM.o Models/Glm/PosteriorSamplers/GammaRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/LogitSampler.o Models/Glm/PosteriorSamplers/LogitSamplerBma.o Models/Glm/PosteriorSamplers/MLAuxMixSampler.o Models/Glm/PosteriorSamplers/MLVS.o Models/Glm/PosteriorSamplers/MLVS_data_imputer.o Models/Glm/PosteriorSamplers/MlogitRwm.o Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.o Models/Glm/PosteriorSamplers/MnpBetaSampler.o Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.o Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.o Models/Glm/PosteriorSamplers/MvRegSampler.o Models/Glm/PosteriorSamplers/MvtRegSampler.o Models/Glm/PosteriorSamplers/NormalMixtureApproximation.o Models/Glm/PosteriorSamplers/PartRegSampler.o Models/Glm/PosteriorSamplers/PoissonDataImputer.o Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.o Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/ProbitRegressionSampler.o Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.o Models/Glm/PosteriorSamplers/RegressionConjSampler.o Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.o Models/Glm/PosteriorSamplers/SpikeSlabSampler.o Models/Glm/PosteriorSamplers/TDataImputer.o Models/Glm/PosteriorSamplers/TRegressionSampler.o Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.o Models/Glm/PosteriorSamplers/VsPriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.o Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.o Models/Glm/PosteriorSamplers/draw_logit_lambda.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_1.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_2.o Models/Glm/PosteriorSamplers/fill_poisson_mixture_approximation_table_3.o Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.o Models/Hierarchical/HierarchicalDirichletModel.o Models/Hierarchical/HierarchicalGammaModel.o Models/Hierarchical/HierarchicalPoissonModel.o Models/Hierarchical/HierarchicalZeroInflatedGammaModel.o Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.o Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.o Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.o Models/HMM/HMM2.o Models/HMM/HealthStateModel.o Models/HMM/HmmDataImputer.o Models/HMM/HmmFilter.o Models/HMM/hmm_tools.o Models/HMM/Clickstream/Event.o Models/HMM/Clickstream/NestedHmm.o Models/HMM/Clickstream/Session.o Models/HMM/Clickstream/Stream.o Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.o Models/HMM/PosteriorSamplers/HmmPosteriorSampler.o Models/IRT/DafePcrDataImputer.o Models/IRT/DafePcrItemSampler.o Models/IRT/DafePcrRwmItemSampler.o Models/IRT/DafePcrRwmSubject.o Models/IRT/DafePcrSubject.o Models/IRT/IRT.o Models/IRT/IrtModel.o Models/IRT/Item.o Models/IRT/PartialCreditModel.o Models/IRT/Subject.o Models/IRT/SubjectPrior.o Models/IRT/SubjectSliceSampler.o LinAlg/Array.o LinAlg/Array3.o LinAlg/ArrayIterator.o LinAlg/Cholesky.o LinAlg/CorrelationMatrix.o LinAlg/DiagonalMatrix.o LinAlg/Eigen.o LinAlg/Givens.o LinAlg/Kronecker.o LinAlg/LU.o LinAlg/LinAlgExceptions.o LinAlg/Matrix.o LinAlg/MatrixPartition.o LinAlg/QR.o LinAlg/SVD.o LinAlg/SWEEP.o LinAlg/Selector.o LinAlg/SpdMatrix.o LinAlg/SubMatrix.o LinAlg/Vector.o LinAlg/VectorView.o LinAlg/blas.o LinAlg/stack_columns.o math/cephes/chbevl.o math/cephes/dawsn.o math/cephes/ei.o math/cephes/expn.o math/cephes/fac.o math/cephes/fresnl.o math/cephes/planck.o math/cephes/polevl.o math/cephes/polylog.o math/cephes/powi.o math/cephes/rgamma.o math/cephes/shichi.o math/cephes/sici.o math/cephes/spence.o math/cephes/zeta.o math/cephes/zetac.o Models/Mixtures/ConditionalFiniteMixtureModel.o Models/Mixtures/DirichletProcessMvnModel.o Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.o Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.o Models/BetaBinomialModel.o Models/BetaModel.o Models/BinomialModel.o Models/CategoricalData.o Models/ChisqModel.o Models/CompositeData.o Models/CompositeModel.o Models/CompositeVectorModel.o Models/ConstrainedVectorParams.o Models/DataTypes.o Models/DirichletModel.o Models/DiscreteUniformModel.o Models/ExponentialModel.o Models/FiniteMixtureModel.o Models/GammaModel.o Models/GaussianModel.o Models/GaussianModelBase.o Models/GaussianModelGivenSigma.o Models/IndependentMvnModel.o Models/IndependentMvnModelGivenScalarSigma.o Models/LognormalModel.o Models/MarginallyUniformCorrelationModel.o Models/MarkovModel.o Models/ModelTypes.o Models/MultinomialModel.o Models/MvnBase.o Models/MvnGivenScalarSigma.o Models/MvnGivenSigma.o Models/MvnModel.o Models/MvtModel.o Models/ParamTypes.o Models/PoissonGammaModel.o Models/PoissonModel.o Models/ProductDirichletModel.o Models/ScaledChisqModel.o Models/SpdData.o Models/SpdModel.o Models/SpdParams.o Models/Sufstat.o Models/TruncatedGammaModel.o Models/UniformCorrelationModel.o Models/UniformModel.o Models/UniformShrinkagePriorModel.o Models/WeightedGaussianSuf.o Models/WeightedMvnModel.o Models/WishartModel.o Models/ZeroInflatedGammaModel.o Models/ZeroInflatedLognormalModel.o Models/ZeroInflatedPoissonModel.o Models/ZeroMeanGaussianModel.o Models/ZeroMeanMvnModel.o Models/Policies/CompositeParamPolicy.o Models/Policies/ManyParamPolicy.o Models/Policies/MixtureDataPolicy.o Models/Policies/NullParamPolicy.o Models/Policies/PriorPolicy.o Models/PosteriorSamplers/AbsorbingMarkovConjSampler.o Models/PosteriorSamplers/BetaBinomialPosteriorSampler.o Models/PosteriorSamplers/BetaBinomialSampler.o Models/PosteriorSamplers/BetaPosteriorSampler.o Models/PosteriorSamplers/CompositeModelSampler.o Models/PosteriorSamplers/CompositeSampler.o Models/PosteriorSamplers/CorrelationSampler.o Models/PosteriorSamplers/DirichletPosteriorSampler.o Models/PosteriorSamplers/ExchangeableDirichletSampler.o Models/PosteriorSamplers/ExponentialGammaSampler.o Models/PosteriorSamplers/FixedProbBinomialSampler.o Models/PosteriorSamplers/GammaPosteriorSampler.o Models/PosteriorSamplers/GaussianConjSampler.o Models/PosteriorSamplers/GaussianMeanSampler.o Models/PosteriorSamplers/GaussianVarSampler.o Models/PosteriorSamplers/GenericGaussianVarianceSampler.o Models/PosteriorSamplers/IndependentMvnConjSampler.o Models/PosteriorSamplers/IndependentMvnVarSampler.o Models/PosteriorSamplers/MarkovConjSampler.o Models/PosteriorSamplers/MarkovConjShrinkageSampler.o Models/PosteriorSamplers/MultinomialDirichletSampler.o Models/PosteriorSamplers/MvnConjSampler.o Models/PosteriorSamplers/MvnIndependentVarianceSampler.o Models/PosteriorSamplers/MvnMeanSampler.o Models/PosteriorSamplers/MvnVarSampler.o Models/PosteriorSamplers/PoissonGammaPosteriorSampler.o Models/PosteriorSamplers/PoissonGammaSampler.o Models/PosteriorSamplers/PosteriorSampler.o Models/PosteriorSamplers/ProductDirichletPosteriorSampler.o Models/PosteriorSamplers/SepStratSampler.o Models/PosteriorSamplers/SharedSigsqSampler.o Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.o Models/PosteriorSamplers/ZeroInflatedPoissonSampler.o Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnConjSampler.o Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.o numopt/Brent.o numopt/Integral.o numopt/Negate.o numopt/NelderMead.o numopt/NumericalDerivatives.o numopt/Powell.o numopt/ScalarLaplaceApproximation.o numopt/ScalarNewtonMax.o numopt/bfgs.o numopt/conj_grad.o numopt/initialize_derivatives.o numopt/max_nd.o numopt/nelder_mead.o numopt/newton.o numopt/simulated_annealing.o Models/PointProcess/BoundedPoissonProcessSimulator.o Models/PointProcess/CosinePoissonProcess.o Models/PointProcess/HomogeneousPoissonProcess.o Models/PointProcess/MarkovModulatedPoissonProcess.o Models/PointProcess/PointProcess.o Models/PointProcess/PoissonClusterProcess.o Models/PointProcess/WeeklyCyclePoissonProcess.o Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.o Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.o boom_r_tools.o create_mixture_component.o create_point_process.o create_poisson_cluster_components.o create_poisson_process.o create_state_model.o determine_nthreads.o extract_mixture_data.o handle_exception.o list_io.o parse_model_formula.o print_R_timestamp.o prior_specification.o seed_rng_from_R.o spike_slab_prior.o Bmath/bd0.o Bmath/beta.o Bmath/chebyshev.o Bmath/choose.o Bmath/d1mach.o Bmath/dbeta.o Bmath/dbinom.o Bmath/dcauchy.o Bmath/dchisq.o Bmath/dexp.o Bmath/df.o Bmath/dgamma.o Bmath/dgeom.o Bmath/dhyper.o Bmath/dlnorm.o Bmath/dlogis.o Bmath/dnbeta.o Bmath/dnbinom.o Bmath/dnchisq.o Bmath/dnorm.o Bmath/dpois.o Bmath/dt.o Bmath/dunif.o Bmath/dweibull.o Bmath/fprec.o Bmath/fround.o Bmath/fsign.o Bmath/ftrunc.o Bmath/gamma_cody.o Bmath/gammalims.o Bmath/i1mach.o Bmath/lbeta.o Bmath/lgammacor.o Bmath/mathlib_error.o Bmath/mlutils.o Bmath/pbeta.o Bmath/pbinom.o Bmath/pcauchy.o Bmath/pchisq.o Bmath/pexp.o Bmath/pf.o Bmath/pgamma.o Bmath/pgeom.o Bmath/phyper.o Bmath/plnorm.o Bmath/plogis.o Bmath/pnbeta.o Bmath/pnbinom.o Bmath/pnchisq.o Bmath/pnf.o Bmath/pnorm.o Bmath/pnt.o Bmath/polygamma.o Bmath/ppois.o Bmath/pt.o Bmath/ptukey.o Bmath/punif.o Bmath/pweibull.o Bmath/qbeta.o Bmath/qbinom.o Bmath/qcauchy.o Bmath/qchisq.o Bmath/qexp.o Bmath/qf.o Bmath/qgamma.o Bmath/qgeom.o Bmath/qhyper.o Bmath/qlnorm.o Bmath/qlogis.o Bmath/qnbinom.o Bmath/qnchisq.o Bmath/qnorm.o Bmath/qpois.o Bmath/qt.o Bmath/qtukey.o Bmath/qunif.o Bmath/qweibull.o Bmath/rbeta.o Bmath/rbinom.o Bmath/rcauchy.o Bmath/rchisq.o Bmath/rexp.o Bmath/rf.o Bmath/rgamma.o Bmath/rgeom.o Bmath/rhyper.o Bmath/rlnorm.o Bmath/rlogis.o Bmath/rmultinom.o Bmath/rnbinom.o Bmath/rnchisq.o Bmath/rnorm.o Bmath/rpois.o Bmath/rt.o Bmath/runif.o Bmath/rweibull.o Bmath/sexp.o Bmath/sign.o Bmath/snorm.o Bmath/stirlerr.o Bmath/toms708.o Bmath/unif_rand.o Samplers/ARMS.o Samplers/DirectProposal.o Samplers/ImportanceResampler.o Samplers/MH_Proposals.o Samplers/MetropolisHastings.o Samplers/MoveAccounting.o Samplers/RejectionSampler.o Samplers/Sampler.o Samplers/ScalarAdaptiveRejectionSampler.o Samplers/ScalarLangevinSampler.o Samplers/ScalarSliceSampler.o Samplers/SliceSampler.o Samplers/TIM.o Samplers/UnivariateLangevinSampler.o Samplers/UnivariateSliceSampler.o Samplers/Gilks/arms.o stats/Bspline.o stats/ChiSquareTest.o stats/DataTable.o stats/Design.o stats/ECDF.o stats/FreqDist.o stats/IQagent.o stats/NaturalSpline.o stats/Resampler.o stats/Spline.o stats/compare_binomial_proportions.o stats/compare_predictions.o stats/diff.o stats/moments.o stats/regression.o stats/simple_random_sample.o Models/StateSpace/AggregatedStateSpaceRegression.o Models/StateSpace/StateSpaceLogitModel.o Models/StateSpace/StateSpaceModel.o Models/StateSpace/StateSpaceModelBase.o Models/StateSpace/StateSpaceNormalMixture.o Models/StateSpace/StateSpacePoissonModel.o Models/StateSpace/StateSpaceRegressionModel.o Models/StateSpace/StateSpaceStudentRegressionModel.o Models/StateSpace/Filters/KalmanTools.o Models/StateSpace/Filters/SparseKalmanTools.o Models/StateSpace/Filters/SparseMatrix.o Models/StateSpace/Filters/SparseVector.o Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.o Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.o Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.o Models/StateSpace/StateModels/ArStateModel.o Models/StateSpace/StateModels/DynamicRegressionStateModel.o Models/StateSpace/StateModels/Holiday.o Models/StateSpace/StateModels/LocalLevelStateModel.o Models/StateSpace/StateModels/LocalLinearTrend.o Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.o Models/StateSpace/StateModels/RandomWalkHolidayStateModel.o Models/StateSpace/StateModels/RegressionStateModel.o Models/StateSpace/StateModels/SeasonalStateModel.o Models/StateSpace/StateModels/StateModel.o Models/StateSpace/StateModels/StudentLocalLinearTrend.o Models/StateSpace/StateModels/TrigStateModel.o TargetFun/JacobianChecker.o TargetFun/LogPost.o TargetFun/ScalarLogpostTF.o TargetFun/TargetFun.o TargetFun/Transformation.o Models/TimeSeries/ArModel.o Models/TimeSeries/NonzeroMeanAr1Model.o Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.o Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.o Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.o cpputil/Constants.o cpputil/Date.o cpputil/DateTime.o cpputil/DefaultVnames.o cpputil/LongString.o cpputil/OutputTable.o cpputil/ParamHolder.o cpputil/Polynomial.o cpputil/Redirector.o cpputil/apply_permutation.o cpputil/cat_string.o cpputil/compare_vector_bool.o cpputil/get_date.o cpputil/gll.o cpputil/infinity.o cpputil/is_all_white.o cpputil/is_numeric.o cpputil/legalize_file_name.o cpputil/lse.o cpputil/parse_range.o cpputil/print_columns.o cpputil/read_file.o cpputil/rep.o cpputil/replace_all.o cpputil/report_error.o cpputil/safelog.o cpputil/split.o cpputil/split_delimited.o cpputil/split_string.o cpputil/str2d.o cpputil/strip.o cpputil/strip_path.o cpputil/strip_white_space.o cpputil/substring_delimited.o cpputil/trim_white_space.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/Boom
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (Boom)

The downloaded source packages are in
	‘/tmp/RtmpsuRmtC/downloaded_packages’

Makevars

all:	libboom.a

# When compiling remotely (e.g. on CRAN's winbuilder) flags to be
# passed to make can be specified here.
# -k:  keep going
# -j 8: use 8 threads
# MAKEFLAGS=" -k -j 8 "

PKG_CFLAGS = -DADD_ -DR_NO_REMAP
PKG_CPPFLAGS = -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE
PKG_LIBS = ${LAPACK_LIBS} ${BLAS_LIBS} ${FLIBS}

############################################################################
# Begin the list of all the BOOM source files.

BART_SRCS := $(wildcard Models/Bart/*.cpp) \
	  $(wildcard Models/Bart/PosteriorSamplers/*.cpp)

DISTRIBUTION_SRCS := $(wildcard distributions/*.cpp)

GLM_SRCS := $(wildcard Models/Glm/*.cpp Models/Glm/PosteriorSamplers/*.cpp)

HIERARCHICAL_SRCS := $(wildcard Models/Hierarchical/*.cpp) \
		  $(wildcard Models/Hierarchical/PosteriorSamplers/*.cpp)

HMM_SRCS := $(wildcard Models/HMM/*.cpp) \
	 $(wildcard Models/HMM/Clickstream/*.cpp) \
	 $(wildcard Models/HMM/Clickstream/PosteriorSamplers/*.cpp) \
	 $(wildcard Models/HMM/PosteriorSamplers/*.cpp)

R_INTERFACE_SRCS := $(wildcard *.cpp)

IRT_SRCS := $(wildcard Models/IRT/*.cpp)

LINALG_SRCS := $(wildcard LinAlg/*.cpp)

MATH_SRCS := $(wildcard math/cephes/*.cpp)

MIXTURE_SRCS := $(wildcard Models/Mixtures/*.cpp) \
	     $(wildcard Models/Mixtures/PosteriorSamplers/*.cpp)

MODELS_SRCS := $(wildcard Models/*.cpp Models/Policies/*.cpp) \
	    $(wildcard Models/PosteriorSamplers/*.cpp)

NUMOPT_SRCS := $(wildcard numopt/*.cpp)

POINTPROCESS_SRCS := $(wildcard Models/PointProcess/*.cpp) \
		  $(wildcard Models/PointProcess/PosteriorSamplers/*.cpp)

RMATH_SRCS := $(wildcard Bmath/*.cpp)

SAMPLERS_SRCS := $(wildcard Samplers/*.cpp Samplers/Gilks/*.cpp)

STATESPACE_SRCS := $(wildcard Models/StateSpace/*.cpp) \
	$(wildcard Models/StateSpace/Filters/*.cpp) \
	$(wildcard Models/StateSpace/PosteriorSamplers/*.cpp) \
	$(wildcard Models/StateSpace/StateModels/*.cpp)

STATS_SRCS := $(wildcard stats/*.cpp)

TARGETFUN_SRCS := $(wildcard TargetFun/*.cpp)

TIMESERIES_SRCS := $(wildcard Models/TimeSeries/*.cpp) \
		$(wildcard Models/TimeSeries/PosteriorSamplers/*.cpp)

UTIL_SRCS := $(wildcard cpputil/*.cpp)


CXX_SRCS = ${BART_SRCS} \
	${DISTRIBUTION_SRCS} \
	${GLM_SRCS} \
	${HIERARCHICAL_SRCS} \
	${HMM_SRCS} \
	${IRT_SRCS} \
	${LINALG_SRCS} \
	${MATH_SRCS} \
	${MIXTURE_SRCS} \
	${MODELS_SRCS} \
	${NUMOPT_SRCS} \
	${POINTPROCESS_SRCS} \
        ${R_INTERFACE_SRCS} \
	${RMATH_SRCS} \
	${SAMPLERS_SRCS} \
	${STATS_SRCS} \
	${STATESPACE_SRCS} \
	${TARGETFUN_SRCS} \
	${TIMESERIES_SRCS} \
	${UTIL_SRCS}

CXX_STD = CXX11

OBJECTS = ${CXX_SRCS:.cpp=.o}

# End list of BOOM source files
############################################################################

libboom.a: ${OBJECTS}
	   ${AR} rc $@ $^

r-cran.mk

#!/usr/bin/make -f
# 							-*- makefile -*-
#
# Generic debian/rules file for the Debian/GNU Linux r-cran-* packages
#
# Should be sufficient for Debianization of CRAN (http://cran.r-project.org) 
# packages. Note that you still need to provide the other files in debian/*,
# in particular control, changelog and copyright. 
# 
# Copyright 2003-2013 by Dirk Eddelbuettel <edd@debian.org>

include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/langcore.mk
## include /usr/share/cdbs/1/rules/dpatch.mk
## include /usr/share/cdbs/1/rules/simple-patchsys.mk

# Check whether source format 3.0 (quilt) is used.  If yes, do not include the conflicting simple-patchsys.mk
formatfile 	:= $(CURDIR)/debian/source/format
format_3_quilt	= $(shell if [ -f $(formatfile) ] ; then if grep -q '3.0[[:space:]]*(quilt)' $(formatfile) ; then echo 1 ; else echo 0 ; fi else echo 0 ; fi )
ifeq ($(format_3_quilt),0)
  include /usr/share/cdbs/1/rules/simple-patchsys.mk
endif

# awk command to extract word after Package or Bundle, not lowercased
awkString	:= "'/^(Package|Bundle):/ {print $$2 }'"

# apply it to the upstream meta-info file DESCRIPTION, also generate a lc version
cranNameOrig    := $(shell awk "$(awkString)" DESCRIPTION)
#cranName        := $(shell echo "$(cranNameOrig)" | tr A-Z a-z | tr . -)
cranName        := $(shell echo "$(cranNameOrig)" | tr A-Z a-z)

## if no debRreposname is known, set default to cran -- thanks, Steffen!
ifeq ($(debRreposname),)
  debRreposname	:= cran
endif

## we can define additional flags for R's make, eg "CXXFLAGS=-g0" for 
## RQuantLib but the default is empty
##   makeFlags	:=
## if makeFlags are defined, then we'll use them in this variable
## which would otherwise be empty
ifneq ($(makeFlags),)
  makeFlagsCall	:= MAKEFLAGS=$(makeFlags)
endif

## and use the results to build the Debian'ized package name
package		:= r-$(debRreposname)-$(cranName)

## awk command to extract word after Priority
prioritystr	:= "'/^Priority:/ {print tolower($$2) }'"
priority        := $(shell awk "$(prioritystr)" DESCRIPTION)

ifeq ($(priority),recommended)
  debRdir	:= usr/lib/R/library
else
  debRdir	:= usr/lib/R/site-library
endif

## current R version in Debian, with thanks to Charles Plessy for the dpkg-query call
#rversion	:= $(shell zcat /usr/share/doc/r-base-dev/changelog.Debian.gz | \
#			dpkg-parsechangelog -l- --count 1  | \
#			awk '/^Version/ {print $$2}')
rversion	:= $(shell dpkg-query -W -f='$${Version}' r-base-dev)

## we use these results for the to-be-installed-in directory
debRlib		:= $(CURDIR)/debian/$(package)/$(debRdir)

## optional installation of a lintian silencer
lintiandir	:= $(CURDIR)/debian/$(package)/usr/share/lintian/overrides

common-install-indep:: R_any_arch
common-install-arch:: R_any_arch

R_any_arch:
                ## create the target directory
		dh_installdirs		$(debRdir)
                ##
                ## support ${R:Depends} via debian/${package}.substvars
		echo "R:Depends=r-base-core (>= ${rversion})" >> debian/$(package).substvars
                ##
                ## call R to install the sources we're looking at
                ## use this inside xvfb-run if this wrapper is installed
		if test -f /usr/bin/xvfb-run; then 			\
			$(makeFlagsCall) xvfb-run -a 			\
				R CMD INSTALL -l $(debRlib) --clean     \
					$(extraInstallFlags) . ;	\
		else							\
			$(makeFlagsCall) R CMD INSTALL -l $(debRlib) 	\
					--clean $(extraInstallFlags) . ;\
		fi
                ## remove extra files which are present in some packages
		rm -vf $(debRlib)/R.css 			\
			$(debRlib)/$(cranNameOrig)/COPYING 	\
			$(debRlib)/$(cranNameOrig)/LICENSE.txt
                ## if we have an overrides file for lintian, install it
		if test -f debian/overrides; then 		\
			install -d $(lintiandir) ; 		\
			install -m 0644 debian/overrides 	\
				$(lintiandir)/$(package); 	\
		fi

## clean target from patch by Steffen Moeller on 16 May 2009
clean::
                ## the re-invocation of a build process should not
                ## leave a footprint in Debian's diff.gz.
		if test -d src; then				\
			find src -regex ".*\.o" |               \
                        xargs --no-run-if-empty -r rm;          \
		fi
		rm -f config.log config.status
                ## the configure file is provided by upstream but
                ## could be recreated by a call to 'autoconf'.
                #if [ -r configure.in ]; then \
                #	rm -f configure \
                #fi
                ##
                # if [ -r src/Makevars.in ]; then \
                # 	rm -f src/Makevars; \
                # fi

Rcpp_reinstall_a.log

> readLines("~/.R/Makevars")
[1] "# CXX=g++-4.8"           "# CXX1X=g++-4.8"        
[3] "# CXX1XFLAGS=-std=c++11"
> install.packages("Rcpp")
Installing package into ‘/home/bearloga/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.7.tar.gz'
Content type 'application/x-gzip' length 2421965 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -I../inst/include/     -fpic  -O3 -pipe  -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -I../inst/include/     -fpic  -O3 -pipe  -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -I../inst/include/     -fpic  -O3 -pipe  -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -I../inst/include/     -fpic  -O3 -pipe  -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -I../inst/include/     -fpic  -O3 -pipe  -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -I../inst/include/     -fpic  -O3 -pipe  -g -c barrier.cpp -o barrier.o
g++ -shared -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /home/bearloga/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)

The downloaded source packages are in
	‘/tmp/RtmpgwlZ9K/downloaded_packages’