[pkgsrc/trunk]: pkgsrc/math/stan-math math/stan-math: Import version 2.17.1

[minskim <minskim%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/40c7d98ef2fe
branches:  trunk
changeset: 383306:40c7d98ef2fe
user:      minskim <minskim%pkgsrc.org@localhost>
date:      Fri Jul 27 06:49:25 2018 +0000

description:
math/stan-math: Import version 2.17.1

The Stan Math Library is a C++, reverse-mode automatic differentiation
library designed to be usable, extensive and extensible, efficient,
scalable, stable, portable, and redistributable in order to facilitate
the construction and utilization of algorithms that utilize
derivatives.

diffstat:

 math/stan-math/DESCR         |     5 +
 math/stan-math/Makefile      |    27 +
 math/stan-math/PLIST         |  1119 ++++++++++++++++++++++++++++++++++++++++++
 math/stan-math/buildlink3.mk |    15 +
 math/stan-math/distinfo      |     6 +
 5 files changed, 1172 insertions(+), 0 deletions(-)

diffs (truncated from 1192 to 300 lines):

diff -r 32828f821a3b -r 40c7d98ef2fe math/stan-math/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/stan-math/DESCR      Fri Jul 27 06:49:25 2018 +0000
@@ -0,0 +1,5 @@
+The Stan Math Library is a C++, reverse-mode automatic differentiation
+library designed to be usable, extensive and extensible, efficient,
+scalable, stable, portable, and redistributable in order to facilitate
+the construction and utilization of algorithms that utilize
+derivatives.
diff -r 32828f821a3b -r 40c7d98ef2fe math/stan-math/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/stan-math/Makefile   Fri Jul 27 06:49:25 2018 +0000
@@ -0,0 +1,27 @@
+# $NetBSD: Makefile,v 1.1 2018/07/27 06:49:25 minskim Exp $
+
+DISTNAME=      stan-math-2.17.1
+CATEGORIES=    math
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=stan-dev/}
+GITHUB_PROJECT=        math
+GITHUB_TAG=    v${PKGVERSION_NOREV}
+
+MAINTAINER=    minskim%NetBSD.org@localhost
+HOMEPAGE=      http://mc-stan.org/
+COMMENT=       Stan Math library
+LICENSE=       modified-bsd
+
+DEPENDS+=      boost-headers>=1.66.0:../../devel/boost-headers
+DEPENDS+=      eigen3>=3.3.3:../../math/eigen3
+DEPENDS+=      sundials>=3.1.1:../../math/sundials
+
+NO_CONFIGURE=  yes
+NO_BUILD=      yes
+USE_TOOLS+=    pax
+
+INSTALLATION_DIRS+=    include/stan
+
+do-install:
+       cd ${WRKSRC} && pax -rw stan ${DESTDIR}${PREFIX}/include
+
+.include "../../mk/bsd.pkg.mk"
diff -r 32828f821a3b -r 40c7d98ef2fe math/stan-math/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/math/stan-math/PLIST      Fri Jul 27 06:49:25 2018 +0000
@@ -0,0 +1,1119 @@
+@comment $NetBSD: PLIST,v 1.1 2018/07/27 06:49:25 minskim Exp $
+include/stan/math.hpp
+include/stan/math/fwd/arr.hpp
+include/stan/math/fwd/arr/fun/log_sum_exp.hpp
+include/stan/math/fwd/arr/fun/sum.hpp
+include/stan/math/fwd/arr/fun/to_fvar.hpp
+include/stan/math/fwd/core.hpp
+include/stan/math/fwd/core/fvar.hpp
+include/stan/math/fwd/core/operator_addition.hpp
+include/stan/math/fwd/core/operator_division.hpp
+include/stan/math/fwd/core/operator_equal.hpp
+include/stan/math/fwd/core/operator_greater_than.hpp
+include/stan/math/fwd/core/operator_greater_than_or_equal.hpp
+include/stan/math/fwd/core/operator_less_than.hpp
+include/stan/math/fwd/core/operator_less_than_or_equal.hpp
+include/stan/math/fwd/core/operator_logical_and.hpp
+include/stan/math/fwd/core/operator_logical_or.hpp
+include/stan/math/fwd/core/operator_multiplication.hpp
+include/stan/math/fwd/core/operator_not_equal.hpp
+include/stan/math/fwd/core/operator_subtraction.hpp
+include/stan/math/fwd/core/operator_unary_minus.hpp
+include/stan/math/fwd/core/operator_unary_not.hpp
+include/stan/math/fwd/core/operator_unary_plus.hpp
+include/stan/math/fwd/core/std_numeric_limits.hpp
+include/stan/math/fwd/mat.hpp
+include/stan/math/fwd/mat/fun/Eigen_NumTraits.hpp
+include/stan/math/fwd/mat/fun/columns_dot_product.hpp
+include/stan/math/fwd/mat/fun/columns_dot_self.hpp
+include/stan/math/fwd/mat/fun/crossprod.hpp
+include/stan/math/fwd/mat/fun/determinant.hpp
+include/stan/math/fwd/mat/fun/divide.hpp
+include/stan/math/fwd/mat/fun/dot_product.hpp
+include/stan/math/fwd/mat/fun/dot_self.hpp
+include/stan/math/fwd/mat/fun/inverse.hpp
+include/stan/math/fwd/mat/fun/log_determinant.hpp
+include/stan/math/fwd/mat/fun/log_softmax.hpp
+include/stan/math/fwd/mat/fun/log_sum_exp.hpp
+include/stan/math/fwd/mat/fun/mdivide_left.hpp
+include/stan/math/fwd/mat/fun/mdivide_left_ldlt.hpp
+include/stan/math/fwd/mat/fun/mdivide_left_tri_low.hpp
+include/stan/math/fwd/mat/fun/mdivide_right.hpp
+include/stan/math/fwd/mat/fun/mdivide_right_tri_low.hpp
+include/stan/math/fwd/mat/fun/multiply.hpp
+include/stan/math/fwd/mat/fun/multiply_lower_tri_self_transpose.hpp
+include/stan/math/fwd/mat/fun/qr_Q.hpp
+include/stan/math/fwd/mat/fun/qr_R.hpp
+include/stan/math/fwd/mat/fun/quad_form_sym.hpp
+include/stan/math/fwd/mat/fun/rows_dot_product.hpp
+include/stan/math/fwd/mat/fun/rows_dot_self.hpp
+include/stan/math/fwd/mat/fun/softmax.hpp
+include/stan/math/fwd/mat/fun/squared_distance.hpp
+include/stan/math/fwd/mat/fun/sum.hpp
+include/stan/math/fwd/mat/fun/tcrossprod.hpp
+include/stan/math/fwd/mat/fun/to_fvar.hpp
+include/stan/math/fwd/mat/fun/trace_gen_quad_form.hpp
+include/stan/math/fwd/mat/fun/trace_quad_form.hpp
+include/stan/math/fwd/mat/fun/typedefs.hpp
+include/stan/math/fwd/mat/fun/unit_vector_constrain.hpp
+include/stan/math/fwd/mat/functor/gradient.hpp
+include/stan/math/fwd/mat/functor/hessian.hpp
+include/stan/math/fwd/mat/functor/jacobian.hpp
+include/stan/math/fwd/mat/meta/operands_and_partials.hpp
+include/stan/math/fwd/mat/vectorize/apply_scalar_unary.hpp
+include/stan/math/fwd/scal.hpp
+include/stan/math/fwd/scal/fun/Phi.hpp
+include/stan/math/fwd/scal/fun/Phi_approx.hpp
+include/stan/math/fwd/scal/fun/abs.hpp
+include/stan/math/fwd/scal/fun/acos.hpp
+include/stan/math/fwd/scal/fun/acosh.hpp
+include/stan/math/fwd/scal/fun/asin.hpp
+include/stan/math/fwd/scal/fun/asinh.hpp
+include/stan/math/fwd/scal/fun/atan.hpp
+include/stan/math/fwd/scal/fun/atan2.hpp
+include/stan/math/fwd/scal/fun/atanh.hpp
+include/stan/math/fwd/scal/fun/bessel_first_kind.hpp
+include/stan/math/fwd/scal/fun/bessel_second_kind.hpp
+include/stan/math/fwd/scal/fun/binary_log_loss.hpp
+include/stan/math/fwd/scal/fun/binomial_coefficient_log.hpp
+include/stan/math/fwd/scal/fun/cbrt.hpp
+include/stan/math/fwd/scal/fun/ceil.hpp
+include/stan/math/fwd/scal/fun/cos.hpp
+include/stan/math/fwd/scal/fun/cosh.hpp
+include/stan/math/fwd/scal/fun/digamma.hpp
+include/stan/math/fwd/scal/fun/erf.hpp
+include/stan/math/fwd/scal/fun/erfc.hpp
+include/stan/math/fwd/scal/fun/exp.hpp
+include/stan/math/fwd/scal/fun/exp2.hpp
+include/stan/math/fwd/scal/fun/expm1.hpp
+include/stan/math/fwd/scal/fun/fabs.hpp
+include/stan/math/fwd/scal/fun/falling_factorial.hpp
+include/stan/math/fwd/scal/fun/fdim.hpp
+include/stan/math/fwd/scal/fun/floor.hpp
+include/stan/math/fwd/scal/fun/fma.hpp
+include/stan/math/fwd/scal/fun/fmax.hpp
+include/stan/math/fwd/scal/fun/fmin.hpp
+include/stan/math/fwd/scal/fun/fmod.hpp
+include/stan/math/fwd/scal/fun/gamma_p.hpp
+include/stan/math/fwd/scal/fun/gamma_q.hpp
+include/stan/math/fwd/scal/fun/grad_inc_beta.hpp
+include/stan/math/fwd/scal/fun/hypot.hpp
+include/stan/math/fwd/scal/fun/inc_beta.hpp
+include/stan/math/fwd/scal/fun/inv.hpp
+include/stan/math/fwd/scal/fun/inv_Phi.hpp
+include/stan/math/fwd/scal/fun/inv_cloglog.hpp
+include/stan/math/fwd/scal/fun/inv_logit.hpp
+include/stan/math/fwd/scal/fun/inv_sqrt.hpp
+include/stan/math/fwd/scal/fun/inv_square.hpp
+include/stan/math/fwd/scal/fun/is_inf.hpp
+include/stan/math/fwd/scal/fun/is_nan.hpp
+include/stan/math/fwd/scal/fun/lbeta.hpp
+include/stan/math/fwd/scal/fun/lgamma.hpp
+include/stan/math/fwd/scal/fun/lmgamma.hpp
+include/stan/math/fwd/scal/fun/log.hpp
+include/stan/math/fwd/scal/fun/log10.hpp
+include/stan/math/fwd/scal/fun/log1m.hpp
+include/stan/math/fwd/scal/fun/log1m_exp.hpp
+include/stan/math/fwd/scal/fun/log1m_inv_logit.hpp
+include/stan/math/fwd/scal/fun/log1p.hpp
+include/stan/math/fwd/scal/fun/log1p_exp.hpp
+include/stan/math/fwd/scal/fun/log2.hpp
+include/stan/math/fwd/scal/fun/log_diff_exp.hpp
+include/stan/math/fwd/scal/fun/log_falling_factorial.hpp
+include/stan/math/fwd/scal/fun/log_inv_logit.hpp
+include/stan/math/fwd/scal/fun/log_mix.hpp
+include/stan/math/fwd/scal/fun/log_rising_factorial.hpp
+include/stan/math/fwd/scal/fun/log_sum_exp.hpp
+include/stan/math/fwd/scal/fun/logit.hpp
+include/stan/math/fwd/scal/fun/modified_bessel_first_kind.hpp
+include/stan/math/fwd/scal/fun/modified_bessel_second_kind.hpp
+include/stan/math/fwd/scal/fun/multiply_log.hpp
+include/stan/math/fwd/scal/fun/owens_t.hpp
+include/stan/math/fwd/scal/fun/pow.hpp
+include/stan/math/fwd/scal/fun/primitive_value.hpp
+include/stan/math/fwd/scal/fun/rising_factorial.hpp
+include/stan/math/fwd/scal/fun/round.hpp
+include/stan/math/fwd/scal/fun/sin.hpp
+include/stan/math/fwd/scal/fun/sinh.hpp
+include/stan/math/fwd/scal/fun/sqrt.hpp
+include/stan/math/fwd/scal/fun/square.hpp
+include/stan/math/fwd/scal/fun/tan.hpp
+include/stan/math/fwd/scal/fun/tanh.hpp
+include/stan/math/fwd/scal/fun/tgamma.hpp
+include/stan/math/fwd/scal/fun/to_fvar.hpp
+include/stan/math/fwd/scal/fun/trigamma.hpp
+include/stan/math/fwd/scal/fun/trunc.hpp
+include/stan/math/fwd/scal/fun/value_of.hpp
+include/stan/math/fwd/scal/fun/value_of_rec.hpp
+include/stan/math/fwd/scal/meta/ad_promotable.hpp
+include/stan/math/fwd/scal/meta/is_fvar.hpp
+include/stan/math/fwd/scal/meta/operands_and_partials.hpp
+include/stan/math/fwd/scal/meta/partials_type.hpp
+include/stan/math/memory/stack_alloc.hpp
+include/stan/math/mix/arr.hpp
+include/stan/math/mix/mat.hpp
+include/stan/math/mix/mat/fun/typedefs.hpp
+include/stan/math/mix/mat/functor/derivative.hpp
+include/stan/math/mix/mat/functor/finite_diff_grad_hessian.hpp
+include/stan/math/mix/mat/functor/grad_hessian.hpp
+include/stan/math/mix/mat/functor/grad_tr_mat_times_hessian.hpp
+include/stan/math/mix/mat/functor/gradient_dot_vector.hpp
+include/stan/math/mix/mat/functor/hessian.hpp
+include/stan/math/mix/mat/functor/hessian_times_vector.hpp
+include/stan/math/mix/mat/functor/partial_derivative.hpp
+include/stan/math/mix/scal.hpp
+include/stan/math/prim/arr.hpp
+include/stan/math/prim/arr/err/check_matching_sizes.hpp
+include/stan/math/prim/arr/err/check_nonzero_size.hpp
+include/stan/math/prim/arr/err/check_ordered.hpp
+include/stan/math/prim/arr/fun/array_builder.hpp
+include/stan/math/prim/arr/fun/common_type.hpp
+include/stan/math/prim/arr/fun/dot.hpp
+include/stan/math/prim/arr/fun/dot_self.hpp
+include/stan/math/prim/arr/fun/fill.hpp
+include/stan/math/prim/arr/fun/inverse_softmax.hpp
+include/stan/math/prim/arr/fun/log_sum_exp.hpp
+include/stan/math/prim/arr/fun/promote_elements.hpp
+include/stan/math/prim/arr/fun/promote_scalar.hpp
+include/stan/math/prim/arr/fun/promote_scalar_type.hpp
+include/stan/math/prim/arr/fun/rep_array.hpp
+include/stan/math/prim/arr/fun/scaled_add.hpp
+include/stan/math/prim/arr/fun/sort_asc.hpp
+include/stan/math/prim/arr/fun/sort_desc.hpp
+include/stan/math/prim/arr/fun/sub.hpp
+include/stan/math/prim/arr/fun/sum.hpp
+include/stan/math/prim/arr/fun/value_of.hpp
+include/stan/math/prim/arr/fun/value_of_rec.hpp
+include/stan/math/prim/arr/functor/coupled_ode_observer.hpp
+include/stan/math/prim/arr/functor/coupled_ode_system.hpp
+include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp
+include/stan/math/prim/arr/meta/VectorBuilderHelper.hpp
+include/stan/math/prim/arr/meta/get.hpp
+include/stan/math/prim/arr/meta/index_type.hpp
+include/stan/math/prim/arr/meta/is_constant_struct.hpp
+include/stan/math/prim/arr/meta/is_vector.hpp
+include/stan/math/prim/arr/meta/length.hpp
+include/stan/math/prim/arr/meta/scalar_type.hpp
+include/stan/math/prim/arr/meta/value_type.hpp
+include/stan/math/prim/mat.hpp
+include/stan/math/prim/mat/err/check_cholesky_factor.hpp
+include/stan/math/prim/mat/err/check_cholesky_factor_corr.hpp
+include/stan/math/prim/mat/err/check_column_index.hpp
+include/stan/math/prim/mat/err/check_corr_matrix.hpp
+include/stan/math/prim/mat/err/check_cov_matrix.hpp
+include/stan/math/prim/mat/err/check_ldlt_factor.hpp
+include/stan/math/prim/mat/err/check_lower_triangular.hpp
+include/stan/math/prim/mat/err/check_matching_dims.hpp
+include/stan/math/prim/mat/err/check_multiplicable.hpp
+include/stan/math/prim/mat/err/check_ordered.hpp
+include/stan/math/prim/mat/err/check_pos_definite.hpp
+include/stan/math/prim/mat/err/check_pos_semidefinite.hpp
+include/stan/math/prim/mat/err/check_positive_ordered.hpp
+include/stan/math/prim/mat/err/check_range.hpp
+include/stan/math/prim/mat/err/check_row_index.hpp
+include/stan/math/prim/mat/err/check_simplex.hpp
+include/stan/math/prim/mat/err/check_spsd_matrix.hpp
+include/stan/math/prim/mat/err/check_square.hpp
+include/stan/math/prim/mat/err/check_std_vector_index.hpp
+include/stan/math/prim/mat/err/check_symmetric.hpp
+include/stan/math/prim/mat/err/check_unit_vector.hpp
+include/stan/math/prim/mat/err/check_vector.hpp
+include/stan/math/prim/mat/err/constraint_tolerance.hpp
+include/stan/math/prim/mat/err/validate_non_negative_index.hpp
+include/stan/math/prim/mat/fun/Eigen.hpp
+include/stan/math/prim/mat/fun/LDLT_factor.hpp
+include/stan/math/prim/mat/fun/MatrixExponential.h
+include/stan/math/prim/mat/fun/Phi.hpp
+include/stan/math/prim/mat/fun/Phi_approx.hpp
+include/stan/math/prim/mat/fun/accumulator.hpp
+include/stan/math/prim/mat/fun/acos.hpp
+include/stan/math/prim/mat/fun/acosh.hpp
+include/stan/math/prim/mat/fun/add.hpp
+include/stan/math/prim/mat/fun/append_array.hpp
+include/stan/math/prim/mat/fun/append_col.hpp
+include/stan/math/prim/mat/fun/append_row.hpp
+include/stan/math/prim/mat/fun/asin.hpp
+include/stan/math/prim/mat/fun/asinh.hpp
+include/stan/math/prim/mat/fun/assign.hpp
+include/stan/math/prim/mat/fun/atan.hpp
+include/stan/math/prim/mat/fun/atanh.hpp
+include/stan/math/prim/mat/fun/autocorrelation.hpp
+include/stan/math/prim/mat/fun/autocovariance.hpp
+include/stan/math/prim/mat/fun/block.hpp
+include/stan/math/prim/mat/fun/cbrt.hpp
+include/stan/math/prim/mat/fun/ceil.hpp
+include/stan/math/prim/mat/fun/cholesky_corr_constrain.hpp
+include/stan/math/prim/mat/fun/cholesky_corr_free.hpp
+include/stan/math/prim/mat/fun/cholesky_decompose.hpp
+include/stan/math/prim/mat/fun/cholesky_factor_constrain.hpp
+include/stan/math/prim/mat/fun/cholesky_factor_free.hpp
+include/stan/math/prim/mat/fun/col.hpp
+include/stan/math/prim/mat/fun/cols.hpp
+include/stan/math/prim/mat/fun/columns_dot_product.hpp
+include/stan/math/prim/mat/fun/columns_dot_self.hpp
+include/stan/math/prim/mat/fun/common_type.hpp
+include/stan/math/prim/mat/fun/corr_matrix_constrain.hpp
+include/stan/math/prim/mat/fun/corr_matrix_free.hpp