From b2aa99496811f78484793ed0ffaf0d1bdd796d03 Mon Sep 17 00:00:00 2001 From: tcberner Date: Tue, 2 May 2017 05:26:40 +0000 Subject: Update math/gsl to 2.3 This release introduces some new features and fixes several bugs: http://savannah.gnu.org/forum/forum.php?forum_id=8751 * update to 2.3 and take maintainership * update math/py-gsl to 2.2.0 for gsl2 support * update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support PR: 218952 Exp-run by: antoine Reviewed by: mat, rakuco Approved by: rakuco (mentor) Differential Revision: https://reviews.freebsd.org/D10522 --- science/afni/Makefile | 2 +- science/fisicalab/Makefile | 2 +- science/getdp/Makefile | 2 +- science/gnudatalanguage/Makefile | 2 +- science/kst2/Makefile | 1 + science/kst2/files/patch-git_a9d24f9 | 106 +++++++++++++++++++++++++++++++++++ science/py-mlpy/Makefile | 2 +- science/step/Makefile | 2 +- 8 files changed, 113 insertions(+), 6 deletions(-) create mode 100644 science/kst2/files/patch-git_a9d24f9 (limited to 'science') diff --git a/science/afni/Makefile b/science/afni/Makefile index cabb4159c8bc..3c40a38ea228 100644 --- a/science/afni/Makefile +++ b/science/afni/Makefile @@ -11,7 +11,7 @@ PORTNAME= afni PORTVERSION= 2015.11.13 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science biology graphics MASTER_SITES= http://www.acadix.biz/Ports/distfiles/ diff --git a/science/fisicalab/Makefile b/science/fisicalab/Makefile index 4dfdf9cdc06c..c90708a04f46 100644 --- a/science/fisicalab/Makefile +++ b/science/fisicalab/Makefile @@ -2,7 +2,7 @@ PORTNAME= fisicalab PORTVERSION= 0.3.3 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science gnustep MASTER_SITES= SAVANNAH diff --git a/science/getdp/Makefile b/science/getdp/Makefile index 34822ea44ba9..00396b5590c3 100644 --- a/science/getdp/Makefile +++ b/science/getdp/Makefile @@ -3,7 +3,7 @@ PORTNAME= getdp PORTVERSION= 2.8.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= http://www.geuz.org/getdp/src/ DISTNAME= ${PORTNAME}-${PORTVERSION}-source diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile index 10b86c1739d6..9d14cd33f953 100644 --- a/science/gnudatalanguage/Makefile +++ b/science/gnudatalanguage/Makefile @@ -3,7 +3,7 @@ PORTNAME= gnudatalanguage DISTVERSION= 0.9.7 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science lang MASTER_SITES= SF/${PORTNAME}/gdl/${PORTVERSION} .if defined(BUILD_PYTHON_MODULE) diff --git a/science/kst2/Makefile b/science/kst2/Makefile index a5fda2435859..b2596e5432e9 100644 --- a/science/kst2/Makefile +++ b/science/kst2/Makefile @@ -3,6 +3,7 @@ PORTNAME= kst DISTVERSION= 2.0.8 +PORTREVISION= 1 CATEGORIES= science kde MASTER_SITES= SF/${PORTNAME}/Kst%20${DISTVERSION:C/-r.*//}/ DISTNAME= Kst-${DISTVERSION} diff --git a/science/kst2/files/patch-git_a9d24f9 b/science/kst2/files/patch-git_a9d24f9 new file mode 100644 index 000000000000..3dd6306cb73b --- /dev/null +++ b/science/kst2/files/patch-git_a9d24f9 @@ -0,0 +1,106 @@ +Backport of: +https://github.com/Kst-plot/kst/commit/a9d24f91057441bbd2e3ed9e7536b071121526cb + +From a9d24f91057441bbd2e3ed9e7536b071121526cb Mon Sep 17 00:00:00 2001 +From: "D. V. Wiebe" +Date: Thu, 10 Mar 2016 14:09:26 -0800 +Subject: [PATCH] GSL-2.x support. + + +--- src/plugins/fits/non_linear.h.orig 2014-02-13 09:41:44 UTC ++++ src/plugins/fits/non_linear.h +@@ -18,6 +18,7 @@ + #include + #include + #include ++#include + #include "common.h" + + struct data { +@@ -100,6 +101,7 @@ bool kstfit_nonlinear( + gsl_multifit_function_fdf function; + gsl_vector_view vectorViewInitial; + gsl_matrix* pMatrixCovariance; ++ gsl_matrix* pMatrixJacobian; + struct data d; + double dXInitial[NUM_PARAMS]; + double* pInputX; +@@ -177,7 +179,16 @@ bool kstfit_nonlinear( + } + iIterations++; + } while( iStatus == GSL_CONTINUE && iIterations < MAX_NUM_ITERATIONS ); +- gsl_multifit_covar( pSolver->J, 0.0, pMatrixCovariance ); ++#if GSL_MAJOR_VERSION >= 2 ++ pMatrixJacobian = gsl_matrix_alloc( iLength, NUM_PARAMS ); ++#else ++ pMatrixJacobian = pSolver->J; ++#endif ++ if ( pMatrixJacobian != NULL ) { ++#if GSL_MAJOR_VERSION >= 2 ++ gsl_multifit_fdfsolver_jac( pSolver, pMatrixJacobian ); ++#endif ++ gsl_multifit_covar( pMatrixJacobian, 0.0, pMatrixCovariance ); + + // + // determine the fitted values... +@@ -207,7 +218,10 @@ bool kstfit_nonlinear( + scalarOutChi->setValue(gsl_blas_dnrm2( pSolver->f )); + + bReturn = true; +- ++#if GSL_MAJOR_VERSION >= 2 ++ gsl_matrix_free( pMatrixJacobian ); ++#endif ++ } + gsl_matrix_free( pMatrixCovariance ); + } + gsl_multifit_fdfsolver_free( pSolver ); +--- src/plugins/fits/non_linear_weighted.h.orig 2014-02-13 09:41:44 UTC ++++ src/plugins/fits/non_linear_weighted.h +@@ -18,6 +18,7 @@ + #include + #include + #include ++#include + #include "common.h" + + struct data { +@@ -101,6 +102,7 @@ bool kstfit_nonlinear_weighted( + gsl_multifit_function_fdf function; + gsl_vector_view vectorViewInitial; + gsl_matrix* pMatrixCovariance; ++ gsl_matrix* pMatrixJacobian; + struct data d; + double dXInitial[NUM_PARAMS]; + double* pInputs[3]; +@@ -193,7 +195,17 @@ bool kstfit_nonlinear_weighted( + } + while( iStatus == GSL_CONTINUE && iIterations < MAX_NUM_ITERATIONS ); + +- gsl_multifit_covar( pSolver->J, 0.0, pMatrixCovariance ); ++#if GSL_MAJOR_VERSION >= 2 ++ pMatrixJacobian = gsl_matrix_alloc( iLength, NUM_PARAMS ); ++#else ++ pMatrixJacobian = pSolver->J; ++#endif ++ ++ if ( pMatrixJacobian != NULL ) { ++#if GSL_MAJOR_VERSION >= 2 ++ gsl_multifit_fdfsolver_jac( pSolver, pMatrixJacobian ); ++#endif ++ gsl_multifit_covar( pMatrixJacobian, 0.0, pMatrixCovariance ); + + // + // determine the fitted values... +@@ -223,7 +235,10 @@ bool kstfit_nonlinear_weighted( + scalarOutChi->setValue(gsl_blas_dnrm2( pSolver->f )); + + bReturn = true; +- ++#if GSL_VERSION_MAJOR >= 2 ++ gsl_matrix_free( pMatrixJacobian ); ++#endif ++ } + gsl_matrix_free( pMatrixCovariance ); + } + gsl_multifit_fdfsolver_free( pSolver ); diff --git a/science/py-mlpy/Makefile b/science/py-mlpy/Makefile index dc362ead1933..7f394aa865f2 100644 --- a/science/py-mlpy/Makefile +++ b/science/py-mlpy/Makefile @@ -3,7 +3,7 @@ PORTNAME= mlpy PORTVERSION= 3.5.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science python MASTER_SITES= SF/${PORTNAME}/${PORTNAME}%20${PORTVERSION} PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/science/step/Makefile b/science/step/Makefile index 5ad4662abb85..d648914cc747 100644 --- a/science/step/Makefile +++ b/science/step/Makefile @@ -2,7 +2,7 @@ PORTNAME= step PORTVERSION= ${KDE4_VERSION} -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science kde kde-kde4 MAINTAINER= kde@FreeBSD.org -- cgit