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Update math/gsl to 2.3

Browse Source 
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
This commit is contained in:
Tobias C. Berner 2017-05-02 05:26:40 +00:00
parent 89a897fcf3
commit 8c99ed5982
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=439928
46 changed files with 301 additions and 39 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
audio/snd/Makefile
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@ -3,6 +3,7 @@
PORTNAME= snd
PORTVERSION= 15.7
PORTREVISION= 1
CATEGORIES= audio
MASTER_SITES= ftp://ccrma-ftp.stanford.edu/pub/Lisp/ \
SF

1
benchmarks/flowgrind/Makefile
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@ -3,6 +3,7 @@
PORTNAME= flowgrind
PORTVERSION= 0.8.0
PORTREVISION= 1
DISTVERSIONPREFIX= ${PORTNAME}-
CATEGORIES= benchmarks

1
biology/bcftools/Makefile
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@ -3,6 +3,7 @@
PORTNAME= bcftools
PORTVERSION= 1.3.1
PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu

2
comms/gnuradio/Makefile
View File

@ -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

2
editors/calligra/Makefile
View File

@ -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}

2
graphics/amide/Makefile
View File

@ -2,7 +2,7 @@
PORTNAME= amide
PORTVERSION= 1.0.5
PORTREVISION= 6
PORTREVISION= 7
CATEGORIES= graphics
MASTER_SITES= SF

44
graphics/amide/files/patch-gsl_2x Normal file
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@ -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++);

2
graphics/enblend/Makefile
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@ -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}

2
graphics/inkscape/Makefile
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@ -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

2
graphics/luminance-qt5/Makefile
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@ -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

2
graphics/luminance/Makefile
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@ -3,7 +3,7 @@
PORTNAME= luminance-hdr
DISTVERSION= 2.3.1
PORTREVISION= 10
PORTREVISION= 11
CATEGORIES= graphics
MASTER_SITES= SF/qtpfsgui/luminance/${DISTVERSION}

1
graphics/nip2/Makefile
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@ -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}/

2
graphics/pfstmo/Makefile
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@ -3,7 +3,7 @@
PORTNAME= pfstmo
PORTVERSION= 1.5
PORTREVISION= 4
PORTREVISION= 5
CATEGORIES= graphics
MASTER_SITES= SF/pfstools/${PORTNAME}/${PORTVERSION}

1
graphics/qgis/Makefile
View File

@ -4,6 +4,7 @@
PORTNAME= qgis
DISTVERSIONPREFIX= final-
DISTVERSION= 2_18_7
PORTREVISION= 1
CATEGORIES= graphics geography
MAINTAINER= rhurlin@gwdg.de

2
graphics/xaos/Makefile
View File

@ -3,7 +3,7 @@
PORTNAME= xaos
PORTVERSION= 3.6
PORTREVISION= 2
PORTREVISION= 3
CATEGORIES= graphics math
MASTER_SITES= SF/${PORTNAME}/XaoS/${PORTVERSION}

1
lang/algol68g/Makefile
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@ -2,6 +2,7 @@
PORTNAME= algol68g
PORTVERSION= 2.8.4
PORTREVISION= 1
CATEGORIES= lang
MASTER_SITES= http://jmvdveer.home.xs4all.nl/

2
mail/bogofilter/Makefile
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@ -3,7 +3,7 @@
PORTNAME= bogofilter
PORTVERSION= 1.2.4
PORTREVISION?= 5
PORTREVISION?= 6
CATEGORIES?= mail
MASTER_SITES= SF/bogofilter/bogofilter-current/bogofilter-${PORTVERSION}

1
math/asymptote/Makefile
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@ -3,6 +3,7 @@
PORTNAME= asymptote
PORTVERSION= 2.37
PORTREVISION= 1
CATEGORIES= math
MASTER_SITES= SF/${PORTNAME}/${PORTVERSION}
DISTNAME= ${PORTNAME}-${PORTVERSION}.src

2
math/dieharder/Makefile
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@ -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

2
math/fflas-ffpack/Makefile
View File

@ -3,7 +3,7 @@
PORTNAME= fflas-ffpack
PORTVERSION= 1.4.3
PORTREVISION= 7
PORTREVISION= 8
CATEGORIES= math
MASTER_SITES= http://linalg.org/ LOCAL/bf

2
math/giacxcas/Makefile
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@ -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/

5
math/gsl/Makefile
View File

@ -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

5
math/gsl/distinfo
View File

@ -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

30
math/gsl/pkg-plist
View File

@ -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

1
math/labplot/Makefile
View File

@ -3,6 +3,7 @@
PORTNAME= labplot
PORTVERSION= 2.4.0
PORTREVISION= 1
DISTVERSIONSUFFIX=-kf5
CATEGORIES= math kde
MASTER_SITES= KDE/stable/${PORTNAME}/${PORTVERSION}

1
math/ocamlgsl/Makefile
View File

@ -4,6 +4,7 @@
PORTNAME= ocaml-gsl
DISTVERSIONPREFIX=v
DISTVERSION= 1.19.1
PORTREVISION= 1
CATEGORIES= math
MAINTAINER= michipili@gmail.com

2
math/octave-forge-gsl/Makefile
View File

@ -3,7 +3,7 @@
PORTNAME= octave-forge-gsl
PORTVERSION= 2.0.0
PORTREVISION= 2
PORTREVISION= 3
CATEGORIES= math
MAINTAINER= stephen@FreeBSD.org

2
math/orpie/Makefile
View File

@ -3,7 +3,7 @@
PORTNAME= orpie
PORTVERSION= 1.5.2
PORTREVISION= 1
PORTREVISION= 2
CATEGORIES+= math
MASTER_SITES= http://pessimization.com/software/orpie/

36
math/orpie/files/patch-gsl_mlgsl__sf.c Normal file
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@ -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)

2
math/p5-Math-GSL/Makefile
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@ -3,7 +3,7 @@
PORTNAME= Math-GSL
PORTVERSION= 0.39
PORTREVISION= 1
PORTREVISION= 2
CATEGORIES= math perl5
MASTER_SITES= CPAN
PKGNAMEPREFIX= p5-

2
math/p5-Math-GSL/pkg-plist
View File

@ -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

1
math/pspp/Makefile
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@ -3,6 +3,7 @@
PORTNAME= pspp
PORTVERSION= 0.10.2
PORTREVISION= 1
CATEGORIES= math
MASTER_SITES= GNU

3
math/py-gsl/Makefile
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@ -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}

5
math/py-gsl/distinfo
View File

@ -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

2
math/qtiplot/Makefile
View File

@ -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/

37
math/qtiplot/files/patch-archgit_c5e8e49 Normal file
View File

@ -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;
}

5
math/rubygem-rb-gsl/Makefile
View File

@ -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)

5
math/rubygem-rb-gsl/distinfo
View File

@ -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

2
science/afni/Makefile
View File

@ -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/

2
science/fisicalab/Makefile
View File

@ -2,7 +2,7 @@
PORTNAME= fisicalab
PORTVERSION= 0.3.3
PORTREVISION= 3
PORTREVISION= 4
CATEGORIES= science gnustep
MASTER_SITES= SAVANNAH

2
science/getdp/Makefile
View File

@ -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

2
science/gnudatalanguage/Makefile
View File

@ -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)

1
science/kst2/Makefile
View File

@ -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}

106
science/kst2/files/patch-git_a9d24f9 Normal file
View File

@ -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 );

2
science/py-mlpy/Makefile
View File

@ -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}

2
science/step/Makefile
View File

@ -2,7 +2,7 @@
PORTNAME= step
PORTVERSION= ${KDE4_VERSION}
PORTREVISION= 2
PORTREVISION= 3
CATEGORIES= science kde kde-kde4
MAINTAINER= kde@FreeBSD.org