Date: Tue, 2 May 2017 05:26:40 +0000 (UTC) From: "Tobias C. Berner" <tcberner@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r439928 - in head: audio/snd benchmarks/flowgrind biology/bcftools comms/gnuradio editors/calligra graphics/amide graphics/amide/files graphics/enblend graphics/inkscape graphics/lumina... Message-ID: <201705020526.v425Qeha070927@repo.freebsd.org>
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Author: tcberner Date: Tue May 2 05:26:40 2017 New Revision: 439928 URL: https://svnweb.freebsd.org/changeset/ports/439928 Log: 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 Added: head/graphics/amide/files/patch-gsl_2x (contents, props changed) head/math/orpie/files/patch-gsl_mlgsl__sf.c (contents, props changed) head/math/qtiplot/files/patch-archgit_c5e8e49 (contents, props changed) head/science/kst2/files/patch-git_a9d24f9 (contents, props changed) Modified: head/audio/snd/Makefile head/benchmarks/flowgrind/Makefile head/biology/bcftools/Makefile head/comms/gnuradio/Makefile head/editors/calligra/Makefile head/graphics/amide/Makefile head/graphics/enblend/Makefile head/graphics/inkscape/Makefile head/graphics/luminance-qt5/Makefile head/graphics/luminance/Makefile head/graphics/nip2/Makefile head/graphics/pfstmo/Makefile head/graphics/qgis/Makefile head/graphics/xaos/Makefile head/lang/algol68g/Makefile head/mail/bogofilter/Makefile head/math/asymptote/Makefile head/math/dieharder/Makefile head/math/fflas-ffpack/Makefile head/math/giacxcas/Makefile head/math/gsl/Makefile head/math/gsl/distinfo head/math/gsl/pkg-plist head/math/labplot/Makefile head/math/ocamlgsl/Makefile head/math/octave-forge-gsl/Makefile head/math/orpie/Makefile head/math/p5-Math-GSL/Makefile head/math/p5-Math-GSL/pkg-plist head/math/pspp/Makefile head/math/py-gsl/Makefile head/math/py-gsl/distinfo head/math/qtiplot/Makefile head/math/rubygem-rb-gsl/Makefile head/math/rubygem-rb-gsl/distinfo head/science/afni/Makefile head/science/fisicalab/Makefile head/science/getdp/Makefile head/science/gnudatalanguage/Makefile head/science/kst2/Makefile head/science/py-mlpy/Makefile head/science/step/Makefile Modified: head/audio/snd/Makefile ============================================================================== --- head/audio/snd/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/audio/snd/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,6 +3,7 @@ PORTNAME= snd PORTVERSION= 15.7 +PORTREVISION= 1 CATEGORIES= audio MASTER_SITES= ftp://ccrma-ftp.stanford.edu/pub/Lisp/ \ SF Modified: head/benchmarks/flowgrind/Makefile ============================================================================== --- head/benchmarks/flowgrind/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/benchmarks/flowgrind/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,6 +3,7 @@ PORTNAME= flowgrind PORTVERSION= 0.8.0 +PORTREVISION= 1 DISTVERSIONPREFIX= ${PORTNAME}- CATEGORIES= benchmarks Modified: head/biology/bcftools/Makefile ============================================================================== --- head/biology/bcftools/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/biology/bcftools/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,6 +3,7 @@ PORTNAME= bcftools PORTVERSION= 1.3.1 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= cartwright@asu.edu Modified: head/comms/gnuradio/Makefile ============================================================================== --- head/comms/gnuradio/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/comms/gnuradio/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,7 +2,7 @@ PORTNAME= gnuradio PORTVERSION= 3.7.10.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= comms astro hamradio MASTER_SITES= http://gnuradio.org/releases/gnuradio/ \ LOCAL/db Modified: head/editors/calligra/Makefile ============================================================================== --- head/editors/calligra/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/editors/calligra/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,7 +2,7 @@ PORTNAME= calligra PORTVERSION= ${CALLIGRA_VERSION} -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= editors kde MASTER_SITES= KDE/${CALLIGRA_BRANCH}/${PORTNAME}-${PORTVERSION}/ DIST_SUBDIR= KDE/${PORTNAME}/${PORTVERSION} Modified: head/graphics/amide/Makefile ============================================================================== --- head/graphics/amide/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/amide/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,7 +2,7 @@ PORTNAME= amide PORTVERSION= 1.0.5 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= graphics MASTER_SITES= SF Added: head/graphics/amide/files/patch-gsl_2x ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/graphics/amide/files/patch-gsl_2x Tue May 2 05:26:40 2017 (r439928) @@ -0,0 +1,44 @@ +Obtained from: +https://sourceforge.net/p/amide/mailman/message/34638848/ + +Description: Fix compilation against GSL >= 2.0 +Author: Gert Wollny <gw.fossdev@gmail.com> +Last-Update: Sun, 22 Nov 2015 14:21:00 +0000 +Bug-Debian: http://bugs.debian.org/805748 + +--- src/tb_profile.c 2015-11-22 14:00:16.361526795 +0100 ++++ src/tb_profile.c 2015-11-22 14:14:58.993881660 +0100 +@@ -32,6 +32,7 @@ + #include "ui_common.h" + #ifdef AMIDE_LIBGSL_SUPPORT + #include <gsl/gsl_multifit_nlin.h> ++#include <gsl/gsl_version.h> + #endif + + +@@ -605,6 +606,7 @@ + result_t * result; + gsl_multifit_fdfsolver * solver; + gsl_matrix *covar; ++ gsl_matrix *J; + gsl_multifit_function_fdf fdf; + gsl_vector * init_p; + gint iter; +@@ -668,8 +670,16 @@ + } + while ((status == GSL_CONTINUE) && (iter < 100)); + ++#if GSL_MAJOR_VERSION > 1 ++ { ++ gsl_matrix *J = gsl_matrix_alloc (result->line->len, num_p);; ++ gsl_multifit_fdfsolver_jac(solver, J); ++ gsl_multifit_covar (J, 0.0, covar); ++ gsl_matrix_free(J); ++ } ++#else + gsl_multifit_covar (solver->J, 0.0, covar); +- ++#endif + j=0; + result->s_fit = gsl_vector_get(solver->x, j++); + result->p_fit = gsl_vector_get(solver->x, j++); Modified: head/graphics/enblend/Makefile ============================================================================== --- head/graphics/enblend/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/enblend/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= enblend PORTVERSION= 4.1.4 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= graphics MASTER_SITES= SF/enblend/enblend-enfuse/enblend-enfuse-${PORTVERSION:R} DISTNAME= enblend-enfuse-${PORTVERSION} Modified: head/graphics/inkscape/Makefile ============================================================================== --- head/graphics/inkscape/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/inkscape/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= inkscape PORTVERSION= 0.92.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= graphics gnome MASTER_SITES= https://media.inkscape.org/dl/resources/file/ \ LOCAL/kwm Modified: head/graphics/luminance-qt5/Makefile ============================================================================== --- head/graphics/luminance-qt5/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/luminance-qt5/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= luminance-hdr DISTVERSION= 2.4.0 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= graphics MASTER_SITES= SF/qtpfsgui/luminance/${DISTVERSION} PKGNAMESUFFIX= -qt5 Modified: head/graphics/luminance/Makefile ============================================================================== --- head/graphics/luminance/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/luminance/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= luminance-hdr DISTVERSION= 2.3.1 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= graphics MASTER_SITES= SF/qtpfsgui/luminance/${DISTVERSION} Modified: head/graphics/nip2/Makefile ============================================================================== --- head/graphics/nip2/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/nip2/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,6 +3,7 @@ PORTNAME= nip2 PORTVERSION= 8.4.0 +PORTREVISION= 1 CATEGORIES= graphics MASTER_SITES= http://www.vips.ecs.soton.ac.uk/supported/${PORTVERSION:R}/ Modified: head/graphics/pfstmo/Makefile ============================================================================== --- head/graphics/pfstmo/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/pfstmo/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= pfstmo PORTVERSION= 1.5 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= graphics MASTER_SITES= SF/pfstools/${PORTNAME}/${PORTVERSION} Modified: head/graphics/qgis/Makefile ============================================================================== --- head/graphics/qgis/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/qgis/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -4,6 +4,7 @@ PORTNAME= qgis DISTVERSIONPREFIX= final- DISTVERSION= 2_18_7 +PORTREVISION= 1 CATEGORIES= graphics geography MAINTAINER= rhurlin@gwdg.de Modified: head/graphics/xaos/Makefile ============================================================================== --- head/graphics/xaos/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/graphics/xaos/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= xaos PORTVERSION= 3.6 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= graphics math MASTER_SITES= SF/${PORTNAME}/XaoS/${PORTVERSION} Modified: head/lang/algol68g/Makefile ============================================================================== --- head/lang/algol68g/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/lang/algol68g/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,6 +2,7 @@ PORTNAME= algol68g PORTVERSION= 2.8.4 +PORTREVISION= 1 CATEGORIES= lang MASTER_SITES= http://jmvdveer.home.xs4all.nl/ Modified: head/mail/bogofilter/Makefile ============================================================================== --- head/mail/bogofilter/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/mail/bogofilter/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= bogofilter PORTVERSION= 1.2.4 -PORTREVISION?= 5 +PORTREVISION?= 6 CATEGORIES?= mail MASTER_SITES= SF/bogofilter/bogofilter-current/bogofilter-${PORTVERSION} Modified: head/math/asymptote/Makefile ============================================================================== --- head/math/asymptote/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/asymptote/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,6 +3,7 @@ PORTNAME= asymptote PORTVERSION= 2.37 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= SF/${PORTNAME}/${PORTVERSION} DISTNAME= ${PORTNAME}-${PORTVERSION}.src Modified: head/math/dieharder/Makefile ============================================================================== --- head/math/dieharder/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/dieharder/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= dieharder PORTVERSION= 3.31.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math MASTER_SITES= http://www.phy.duke.edu/~rgb/General/dieharder/ LOCAL/bf Modified: head/math/fflas-ffpack/Makefile ============================================================================== --- head/math/fflas-ffpack/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/fflas-ffpack/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= fflas-ffpack PORTVERSION= 1.4.3 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= math MASTER_SITES= http://linalg.org/ LOCAL/bf Modified: head/math/giacxcas/Makefile ============================================================================== --- head/math/giacxcas/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/giacxcas/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= giacxcas DISTVERSION= 1.2.2-57 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MASTER_SITES= http://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/:giac \ http://www-fourier.ujf-grenoble.fr/~parisse/giac/freebsd/ Modified: head/math/gsl/Makefile ============================================================================== --- head/math/gsl/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/gsl/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,12 +2,11 @@ # $FreeBSD$ PORTNAME= gsl -PORTVERSION= 1.16 -PORTREVISION= 2 +PORTVERSION= 2.3 CATEGORIES= math MASTER_SITES= GNU -MAINTAINER= ports@FreeBSD.org +MAINTAINER= tcberner@FreeBSD.org COMMENT= The GNU Scientific Library - mathematical libs LICENSE= GPLv3 Modified: head/math/gsl/distinfo ============================================================================== --- head/math/gsl/distinfo Tue May 2 05:02:52 2017 (r439927) +++ head/math/gsl/distinfo Tue May 2 05:26:40 2017 (r439928) @@ -1,2 +1,3 @@ -SHA256 (gsl-1.16.tar.gz) = 73bc2f51b90d2a780e6d266d43e487b3dbd78945dd0b04b14ca5980fe28d2f53 -SIZE (gsl-1.16.tar.gz) = 3534080 +TIMESTAMP = 1493276070 +SHA256 (gsl-2.3.tar.gz) = 562500b789cd599b3a4f88547a7a3280538ab2ff4939504c8b4ac4ca25feadfb +SIZE (gsl-2.3.tar.gz) = 4510731 Modified: head/math/gsl/pkg-plist ============================================================================== --- head/math/gsl/pkg-plist Tue May 2 05:02:52 2017 (r439927) +++ head/math/gsl/pkg-plist Tue May 2 05:26:40 2017 (r439928) @@ -54,6 +54,7 @@ include/gsl/gsl_ieee_utils.h include/gsl/gsl_inline.h include/gsl/gsl_integration.h include/gsl/gsl_interp.h +include/gsl/gsl_interp2d.h include/gsl/gsl_linalg.h include/gsl/gsl_machine.h include/gsl/gsl_math.h @@ -82,6 +83,9 @@ include/gsl/gsl_monte_plain.h include/gsl/gsl_monte_vegas.h include/gsl/gsl_multifit.h include/gsl/gsl_multifit_nlin.h +include/gsl/gsl_multifit_nlinear.h +include/gsl/gsl_multilarge.h +include/gsl/gsl_multilarge_nlinear.h include/gsl/gsl_multimin.h include/gsl/gsl_multiroots.h include/gsl/gsl_multiset.h @@ -100,6 +104,21 @@ include/gsl/gsl_permute_float.h include/gsl/gsl_permute_int.h include/gsl/gsl_permute_long.h include/gsl/gsl_permute_long_double.h +include/gsl/gsl_permute_matrix.h +include/gsl/gsl_permute_matrix_char.h +include/gsl/gsl_permute_matrix_complex_double.h +include/gsl/gsl_permute_matrix_complex_float.h +include/gsl/gsl_permute_matrix_complex_long_double.h +include/gsl/gsl_permute_matrix_double.h +include/gsl/gsl_permute_matrix_float.h +include/gsl/gsl_permute_matrix_int.h +include/gsl/gsl_permute_matrix_long.h +include/gsl/gsl_permute_matrix_long_double.h +include/gsl/gsl_permute_matrix_short.h +include/gsl/gsl_permute_matrix_uchar.h +include/gsl/gsl_permute_matrix_uint.h +include/gsl/gsl_permute_matrix_ulong.h +include/gsl/gsl_permute_matrix_ushort.h include/gsl/gsl_permute_short.h include/gsl/gsl_permute_uchar.h include/gsl/gsl_permute_uint.h @@ -127,6 +146,7 @@ include/gsl/gsl_qrng.h include/gsl/gsl_randist.h include/gsl/gsl_rng.h include/gsl/gsl_roots.h +include/gsl/gsl_rstat.h include/gsl/gsl_sf.h include/gsl/gsl_sf_airy.h include/gsl/gsl_sf_bessel.h @@ -183,8 +203,12 @@ include/gsl/gsl_sort_vector_uchar.h include/gsl/gsl_sort_vector_uint.h include/gsl/gsl_sort_vector_ulong.h include/gsl/gsl_sort_vector_ushort.h +include/gsl/gsl_spblas.h include/gsl/gsl_specfunc.h +include/gsl/gsl_splinalg.h include/gsl/gsl_spline.h +include/gsl/gsl_spline2d.h +include/gsl/gsl_spmatrix.h include/gsl/gsl_statistics.h include/gsl/gsl_statistics_char.h include/gsl/gsl_statistics_double.h @@ -222,15 +246,15 @@ include/gsl/gsl_wavelet.h include/gsl/gsl_wavelet2d.h lib/libgsl.a lib/libgsl.so -lib/libgsl.so.0 -lib/libgsl.so.0.17.0 +lib/libgsl.so.19 +lib/libgsl.so.19.3.0 lib/libgslcblas.a lib/libgslcblas.so lib/libgslcblas.so.0 lib/libgslcblas.so.0.0.0 libdata/pkgconfig/gsl.pc -share/aclocal/gsl.m4 man/man1/gsl-config.1.gz man/man1/gsl-histogram.1.gz man/man1/gsl-randist.1.gz man/man3/gsl.3.gz +share/aclocal/gsl.m4 Modified: head/math/labplot/Makefile ============================================================================== --- head/math/labplot/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/labplot/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,6 +3,7 @@ PORTNAME= labplot PORTVERSION= 2.4.0 +PORTREVISION= 1 DISTVERSIONSUFFIX=-kf5 CATEGORIES= math kde MASTER_SITES= KDE/stable/${PORTNAME}/${PORTVERSION} Modified: head/math/ocamlgsl/Makefile ============================================================================== --- head/math/ocamlgsl/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/ocamlgsl/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -4,6 +4,7 @@ PORTNAME= ocaml-gsl DISTVERSIONPREFIX=v DISTVERSION= 1.19.1 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= michipili@gmail.com Modified: head/math/octave-forge-gsl/Makefile ============================================================================== --- head/math/octave-forge-gsl/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/octave-forge-gsl/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= octave-forge-gsl PORTVERSION= 2.0.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MAINTAINER= stephen@FreeBSD.org Modified: head/math/orpie/Makefile ============================================================================== --- head/math/orpie/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/orpie/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= orpie PORTVERSION= 1.5.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES+= math MASTER_SITES= http://pessimization.com/software/orpie/ Added: head/math/orpie/files/patch-gsl_mlgsl__sf.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/orpie/files/patch-gsl_mlgsl__sf.c Tue May 2 05:26:40 2017 (r439928) @@ -0,0 +1,36 @@ +Obtained from: +https://sources.debian.net/src/orpie/1.5.2-1/debian/patches/gsl-fix/ + +Description: fix some incompatibilities with libgsl 2.1 +Author: Uwe Steinmann <steinm@debian.org> +Forwarded: not-needed + +--- gsl/mlgsl_sf.c.orig 2014-04-12 01:43:31 UTC ++++ gsl/mlgsl_sf.c +@@ -258,7 +258,8 @@ SF2(ellint_Dcomp, Double_val, GSL_MODE_v + SF3(ellint_F, Double_val, Double_val, GSL_MODE_val) + SF3(ellint_E, Double_val, Double_val, GSL_MODE_val) + SF4(ellint_P, Double_val, Double_val, Double_val, GSL_MODE_val) +-SF4(ellint_D, Double_val, Double_val, Double_val, GSL_MODE_val) ++//SF4(ellint_D, Double_val, Double_val, Double_val, GSL_MODE_val) ++SF3(ellint_D, Double_val, Double_val, GSL_MODE_val) + SF3(ellint_RC, Double_val, Double_val, GSL_MODE_val) + SF4(ellint_RD, Double_val, Double_val, Double_val, GSL_MODE_val) + SF4(ellint_RF, Double_val, Double_val, Double_val, GSL_MODE_val) +@@ -452,6 +453,7 @@ SF1(legendre_Q1, Double_val) + SF2(legendre_Ql, Int_val, Double_val) + + /* Associated Legendre Polynomials and Spherical Harmonics */ ++/* + SF3(legendre_Plm, Int_val, Int_val, Double_val) + CAMLprim value + ml_gsl_sf_legendre_Plm_array(value lmax, value m, value x, value result_array) +@@ -487,7 +489,7 @@ ml_gsl_sf_legendre_array_size(value lmax + ret = Val_int(gsl_ret); + CAMLreturn(ret); + } +- ++*/ + /* LOGARITHM and related functions */ + SF1(log, Double_val) + SF1(log_abs, Double_val) Modified: head/math/p5-Math-GSL/Makefile ============================================================================== --- head/math/p5-Math-GSL/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/p5-Math-GSL/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= Math-GSL PORTVERSION= 0.39 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- Modified: head/math/p5-Math-GSL/pkg-plist ============================================================================== --- head/math/p5-Math-GSL/pkg-plist Tue May 2 05:02:52 2017 (r439927) +++ head/math/p5-Math-GSL/pkg-plist Tue May 2 05:26:40 2017 (r439928) @@ -79,6 +79,8 @@ %%SITE_ARCH%%/auto/Math/GSL/MatrixComplex/MatrixComplex.so %%SITE_ARCH%%/auto/Math/GSL/Min/Min.so %%SITE_ARCH%%/auto/Math/GSL/Monte/Monte.so +%%SITE_ARCH%%/auto/Math/GSL/Multifit/Multifit.so +%%SITE_ARCH%%/auto/Math/GSL/Multilarge/Multilarge.so %%SITE_ARCH%%/auto/Math/GSL/Multimin/Multimin.so %%SITE_ARCH%%/auto/Math/GSL/Multiroots/Multiroots.so %%SITE_ARCH%%/auto/Math/GSL/NTuple/NTuple.so Modified: head/math/pspp/Makefile ============================================================================== --- head/math/pspp/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/pspp/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,6 +3,7 @@ PORTNAME= pspp PORTVERSION= 0.10.2 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= GNU Modified: head/math/py-gsl/Makefile ============================================================================== --- head/math/py-gsl/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/py-gsl/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= gsl -PORTVERSION= 2.1.1 -PORTREVISION= 1 +PORTVERSION= 2.2.0 CATEGORIES= math python MASTER_SITES= SF/py${PORTNAME}/py${PORTNAME}/py${PORTNAME}-${PORTVERSION} PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} Modified: head/math/py-gsl/distinfo ============================================================================== --- head/math/py-gsl/distinfo Tue May 2 05:02:52 2017 (r439927) +++ head/math/py-gsl/distinfo Tue May 2 05:26:40 2017 (r439928) @@ -1,2 +1,3 @@ -SHA256 (python/pygsl-2.1.1.tar.gz) = 3d17e6deb5433b331a567a45ff467f41e9059def76e6ef0f21d8e891498f946a -SIZE (python/pygsl-2.1.1.tar.gz) = 727636 +TIMESTAMP = 1493448013 +SHA256 (python/pygsl-2.2.0.tar.gz) = 200e7986c368cb815685e502993e5211702219e1a0bb79030d671c35df25a59e +SIZE (python/pygsl-2.2.0.tar.gz) = 983467 Modified: head/math/qtiplot/Makefile ============================================================================== --- head/math/qtiplot/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/qtiplot/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -3,7 +3,7 @@ PORTNAME= qtiplot DISTVERSION= 0.9.8.9 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= math science MASTER_SITES= BERLIOS http://soft.proindependent.com/src/ Added: head/math/qtiplot/files/patch-archgit_c5e8e49 ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/math/qtiplot/files/patch-archgit_c5e8e49 Tue May 2 05:26:40 2017 (r439928) @@ -0,0 +1,37 @@ +Obtained from: +https://git.archlinux.org/svntogit/packages.git/tree/trunk/qtiplot-gsl2.patch?h=packages/qtiplot + +Description: adoptation to gsl2. +Author: Damir Islamov <damir@secretlaboratory.ru> +Last-Update: 2015-12-04 + +--- qtiplot/src/analysis/Fit.cpp ++++ qtiplot/src/analysis/Fit.cpp +@@ -126,10 +126,12 @@ gsl_multifit_fdfsolver * Fit::fitGSL(gsl + break; + } + } +- ++ gsl_matrix *J = gsl_matrix_alloc(d_n, d_p); + if (status){ +- gsl_multifit_covar (s->J, 0.0, covar); ++ gsl_multifit_fdfsolver_jac(s, J); ++ gsl_multifit_covar (J, 0.0, covar); + iterations = 0; ++ gsl_matrix_free (J); + return s; + } + +@@ -154,9 +156,9 @@ gsl_multifit_fdfsolver * Fit::fitGSL(gsl + + status = gsl_multifit_test_delta (s->dx, s->x, d_tolerance, d_tolerance); + } while (inRange && status == GSL_CONTINUE && (int)iter < d_max_iterations); +- +- gsl_multifit_covar (s->J, 0.0, covar); +- ++ gsl_multifit_fdfsolver_jac(s, J); ++ gsl_multifit_covar (J, 0.0, covar); ++ gsl_matrix_free (J); + iterations = iter; + return s; + } Modified: head/math/rubygem-rb-gsl/Makefile ============================================================================== --- head/math/rubygem-rb-gsl/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/math/rubygem-rb-gsl/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -1,10 +1,11 @@ # Created by: Shin-ya MURAKAMI <murashin@gfd-dennou.org> # $FreeBSD$ -PORTNAME= rb-gsl -PORTVERSION= 1.16.0.4 +PORTNAME= gsl +PORTVERSION= 2.1.0.2 CATEGORIES= math rubygems MASTER_SITES= RG +PKGNAMEPREFIX= rubygem-rb- MAINTAINER= murashin@gfd-dennou.org COMMENT= Ruby extension library for GSL (GNU Scientific Library) Modified: head/math/rubygem-rb-gsl/distinfo ============================================================================== --- head/math/rubygem-rb-gsl/distinfo Tue May 2 05:02:52 2017 (r439927) +++ head/math/rubygem-rb-gsl/distinfo Tue May 2 05:26:40 2017 (r439928) @@ -1,2 +1,3 @@ -SHA256 (rubygem/rb-gsl-1.16.0.4.gem) = bc6573cc36410d2ec88672d4b12e2c908684796b276a8743c19345bbb44bef94 -SIZE (rubygem/rb-gsl-1.16.0.4.gem) = 588288 +TIMESTAMP = 1493451497 +SHA256 (rubygem/gsl-2.1.0.2.gem) = bb748021a950ae51a7f0eeadffbcd9b039734fcbb99a04a313ca48c4e60dd9ba +SIZE (rubygem/gsl-2.1.0.2.gem) = 735232 Modified: head/science/afni/Makefile ============================================================================== --- head/science/afni/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/science/afni/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -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/ Modified: head/science/fisicalab/Makefile ============================================================================== --- head/science/fisicalab/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/science/fisicalab/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,7 +2,7 @@ PORTNAME= fisicalab PORTVERSION= 0.3.3 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science gnustep MASTER_SITES= SAVANNAH Modified: head/science/getdp/Makefile ============================================================================== --- head/science/getdp/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/science/getdp/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -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 Modified: head/science/gnudatalanguage/Makefile ============================================================================== --- head/science/gnudatalanguage/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/science/gnudatalanguage/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -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) Modified: head/science/kst2/Makefile ============================================================================== --- head/science/kst2/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/science/kst2/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -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} Added: head/science/kst2/files/patch-git_a9d24f9 ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/kst2/files/patch-git_a9d24f9 Tue May 2 05:26:40 2017 (r439928) @@ -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" <dvw@ketiltrout.net> +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 <gsl/gsl_blas.h> + #include <gsl/gsl_multifit_nlin.h> + #include <gsl/gsl_statistics.h> ++#include <gsl/gsl_version.h> + #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 <gsl/gsl_blas.h> + #include <gsl/gsl_multifit_nlin.h> + #include <gsl/gsl_statistics.h> ++#include <gsl/gsl_version.h> + #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 ); Modified: head/science/py-mlpy/Makefile ============================================================================== --- head/science/py-mlpy/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/science/py-mlpy/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -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} Modified: head/science/step/Makefile ============================================================================== --- head/science/step/Makefile Tue May 2 05:02:52 2017 (r439927) +++ head/science/step/Makefile Tue May 2 05:26:40 2017 (r439928) @@ -2,7 +2,7 @@ PORTNAME= step PORTVERSION= ${KDE4_VERSION} -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science kde kde-kde4 MAINTAINER= kde@FreeBSD.org
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