[DRE-commits] [ruby-gsl] 01/08: add patches for gsl 2
Cédric Boutillier
boutil at moszumanska.debian.org
Mon Feb 29 14:39:07 UTC 2016
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boutil pushed a commit to branch master
in repository ruby-gsl.
commit 45afc524eed684c3143399014dbbca543911c2b8
Author: Cédric Boutillier <boutil at debian.org>
Date: Mon Feb 29 14:54:08 2016 +0100
add patches for gsl 2
---
debian/patches/gsl2_multifit.patch | 172 ++++++++++++++++++++++++++++
debian/patches/gsl2_special_functions.patch | 120 +++++++++++++++++++
debian/patches/gsl2_tamu_anova.patch | 20 ++++
debian/patches/series | 3 +
4 files changed, 315 insertions(+)
diff --git a/debian/patches/gsl2_multifit.patch b/debian/patches/gsl2_multifit.patch
new file mode 100644
index 0000000..1a48324
--- /dev/null
+++ b/debian/patches/gsl2_multifit.patch
@@ -0,0 +1,172 @@
+Description: expicitly compute Jacobians of fdfsolver structs
+ as it is no more available as a J member in GSL 2.x
+Author: Cédric Boutillier <boutil at debian.org>
+Origin: vendor
+Bug-Debian: https://bugs.debian.org/804499
+Bug: https://github.com/SciRuby/rb-gsl/issues/24
+Forwarded: https://github.com/SciRuby/rb-gsl/pull/31
+Last-Update: 2016-02-29
+
+--- a/ext/gsl_native/histogram.c
++++ b/ext/gsl_native/histogram.c
+@@ -1169,6 +1169,7 @@
+ size_t n, dof; /* # of data points */
+ size_t p = 3; /* # of fitting parameters */
+ gsl_multifit_function_fdf f;
++ gsl_matrix *J = NULL;
+ gsl_matrix *covar = NULL;
+ gsl_vector *x = NULL;
+ double sigma, mean, height, errs, errm, errh, chi2;
+@@ -1197,6 +1198,7 @@
+ hh.binend = binend;
+ n = binend - binstart + 1;
+
++ J = gsl_matrix_alloc(n, p);
+ covar = gsl_matrix_alloc(p, p);
+
+ f.f = Gaussian_f;
+@@ -1219,7 +1221,8 @@
+ sigma = sqrt(gsl_vector_get(s->x, 0));
+ mean = gsl_vector_get(s->x, 1);
+ height = gsl_vector_get(s->x, 2)*sigma*sqrt(2*M_PI);
+- gsl_multifit_covar(s->J, 0.0, covar);
++ gsl_multifit_fdfsolver_jac(s, J);
++ gsl_multifit_covar(J, 0.0, covar);
+ chi2 = gsl_pow_2(gsl_blas_dnrm2(s->f)); /* not reduced chi-square */
+ dof = n - p;
+ errs = sqrt(chi2/dof*gsl_matrix_get(covar, 0, 0))/sigma/2;
+@@ -1305,6 +1308,7 @@
+ size_t n, dof; /* # of data points */
+ size_t p = 2; /* # of fitting parameters */
+ gsl_multifit_function_fdf f;
++ gsl_matrix *J = NULL;
+ gsl_matrix *covar = NULL;
+ gsl_vector *x = NULL;
+ double sigma, height, errs, errh, chi2;
+@@ -1332,6 +1336,7 @@
+ hh.binend = binend;
+ n = binend - binstart + 1;
+
++ J = gsl_matrix_alloc(n, p);
+ covar = gsl_matrix_alloc(p, p);
+
+ f.f = Rayleigh_f;
+@@ -1353,7 +1358,8 @@
+ } while (status == GSL_CONTINUE);
+ sigma = sqrt(gsl_vector_get(s->x, 0));
+ height = gsl_vector_get(s->x, 1)*sigma*sigma;
+- gsl_multifit_covar(s->J, 0.0, covar);
++ gsl_multifit_fdfsolver_jac(s, J);
++ gsl_multifit_covar(J, 0.0, covar);
+ chi2 = gsl_pow_2(gsl_blas_dnrm2(s->f)); /* not reduced chi-square */
+ dof = n - p;
+ errs = sqrt(chi2/dof*gsl_matrix_get(covar, 0, 0))/sigma/2;
+@@ -1441,6 +1447,7 @@
+ size_t n, dof; /* # of data points */
+ size_t p = 2; /* # of fitting parameters */
+ gsl_multifit_function_fdf f;
++ gsl_matrix *J = NULL;
+ gsl_matrix *covar = NULL;
+ gsl_vector *x = NULL;
+ double b, height, errs, errh, chi2;
+@@ -1468,6 +1475,7 @@
+ hh.binend = binend;
+ n = binend - binstart + 1;
+
++ J = gsl_matrix_alloc(n, p);
+ covar = gsl_matrix_alloc(p, p);
+
+ f.f = xExponential_f;
+@@ -1489,7 +1497,8 @@
+ } while (status == GSL_CONTINUE);
+ b = gsl_vector_get(s->x, 0);
+ height = gsl_vector_get(s->x, 1);
+- gsl_multifit_covar(s->J, 0.0, covar);
++ gsl_multifit_fdfsolver_jac(s, J);
++ gsl_multifit_covar(J, 0.0, covar);
+ chi2 = gsl_pow_2(gsl_blas_dnrm2(s->f)); /* not reduced chi-square */
+ dof = n - p;
+ errs = sqrt(chi2/dof*gsl_matrix_get(covar, 0, 0));
+--- a/ext/gsl_native/multifit.c
++++ b/ext/gsl_native/multifit.c
+@@ -324,6 +324,7 @@
+ {
+ gsl_multifit_fdfsolver *solver = NULL;
+ gsl_vector *g = NULL;
++ gsl_matrix *J = NULL;
+ int status;
+ double epsabs;
+ Data_Get_Struct(obj, gsl_multifit_fdfsolver, solver);
+@@ -331,7 +332,9 @@
+ case 1:
+ Need_Float(argv[0]);
+ g = gsl_vector_alloc(solver->x->size);
+- gsl_multifit_gradient(solver->J, solver->f, g);
++ J = gsl_matrix_alloc(solver->f->size, solver->x->size);
++ gsl_multifit_fdfsolver_jac(solver, J);
++ gsl_multifit_gradient(J, solver->f, g);
+ epsabs = NUM2DBL(argv[0]);
+ status = gsl_multifit_test_gradient(g, epsabs);
+ gsl_vector_free(g);
+@@ -353,15 +356,17 @@
+ {
+ gsl_multifit_fdfsolver *solver = NULL;
+ gsl_vector *g = NULL;
++ gsl_matrix *J = gsl_matrix_alloc(solver->f->size, solver->x->size);
+ // local variable "status" declared and set, but never used
+ //int status;
+ Data_Get_Struct(obj, gsl_multifit_fdfsolver, solver);
++ gsl_multifit_fdfsolver_jac(solver, J);
+ if (argc == 1) {
+ Data_Get_Vector(argv[0], g);
+- return INT2FIX(gsl_multifit_gradient(solver->J, solver->f, g));
++ return INT2FIX(gsl_multifit_gradient(J, solver->f, g));
+ } else {
+ g = gsl_vector_alloc(solver->x->size);
+- /*status =*/ gsl_multifit_gradient(solver->J, solver->f, g);
++ /*status =*/ gsl_multifit_gradient(J, solver->f, g);
+ return Data_Wrap_Struct(cgsl_vector, 0, gsl_vector_free, g);
+ }
+ }
+@@ -377,15 +382,17 @@
+ Need_Float(argv[0]);
+ Data_Get_Struct(obj, gsl_multifit_fdfsolver, solver);
+ epsrel = NUM2DBL(argv[0]);
++ gsl_matrix *J = gsl_matrix_alloc(solver->f->size, solver->x->size);
++ gsl_multifit_fdfsolver_jac(solver, J);
+ switch (argc) {
+ case 1:
+ covar = gsl_matrix_alloc(solver->x->size, solver->x->size);
+- /*status =*/ gsl_multifit_covar(solver->J, epsrel, covar);
++ /*status =*/ gsl_multifit_covar(J, epsrel, covar);
+ return Data_Wrap_Struct(cgsl_matrix, 0, gsl_matrix_free, covar);
+ break;
+ case 2:
+ Data_Get_Matrix(argv[1], covar);
+- return INT2FIX(gsl_multifit_covar(solver->J, epsrel, covar));
++ return INT2FIX(gsl_multifit_covar(J, epsrel, covar));
+ break;
+ default:
+ rb_raise(rb_eArgError, "wrong number of arguments");
+@@ -418,7 +425,9 @@
+ {
+ gsl_multifit_fdfsolver *solver = NULL;
+ Data_Get_Struct(obj, gsl_multifit_fdfsolver, solver);
+- return Data_Wrap_Struct(cgsl_matrix_view_ro, 0, NULL, solver->J);
++ gsl_matrix *J = gsl_matrix_alloc(solver->f->size, solver->x->size);
++ gsl_multifit_fdfsolver_jac(solver, J);
++ return Data_Wrap_Struct(cgsl_matrix_view_ro, 0, NULL, J);
+ }
+
+ /* singleton */
+@@ -1699,7 +1708,9 @@
+ covar = gsl_matrix_alloc(p, p);
+ chi2 = gsl_pow_2(gsl_blas_dnrm2(solver->f)); /* not reduced chi-square */
+ dof = n - p;
+- gsl_multifit_covar(solver->J, 0.0, covar);
++ gsl_matrix *J = gsl_matrix_alloc(n,p);
++ gsl_multifit_fdfsolver_jac(solver, J);
++ gsl_multifit_covar(J, 0.0, covar);
+ for (i = 0; i < p; i++)
+ gsl_vector_set(verr, i, sqrt(chi2/dof*gsl_matrix_get(covar, i, i)));
+ gsl_matrix_free(covar);
diff --git a/debian/patches/gsl2_special_functions.patch b/debian/patches/gsl2_special_functions.patch
new file mode 100644
index 0000000..7d59065
--- /dev/null
+++ b/debian/patches/gsl2_special_functions.patch
@@ -0,0 +1,120 @@
+Description: adapt to changes in special functions in GSL 2.x
+ - change names of some special returning error codes (_e suffix)
+ - drop n parameter for elliptic_D function
+Author: Cédric Boutillier <boutil at debian.org>
+Origin: vendor
+Bug-Debian: https://bugs.debian.org/804499
+Bug: https://github.com/SciRuby/rb-gsl/issues/24
+Forwarded: https://github.com/SciRuby/rb-gsl/pull/31
+Last-Update: 2016-02-29
+
+--- a/ext/gsl_native/sf_mathieu.c
++++ b/ext/gsl_native/sf_mathieu.c
+@@ -133,11 +133,11 @@
+ /**********/
+ static VALUE rb_gsl_sf_mathieu_a_e(VALUE module, VALUE order, VALUE qq)
+ {
+- return rb_gsl_sf_eval_e_int_double(gsl_sf_mathieu_a, order, qq);
++ return rb_gsl_sf_eval_e_int_double(gsl_sf_mathieu_a_e, order, qq);
+ }
+ static VALUE rb_gsl_sf_mathieu_a(VALUE module, VALUE order, VALUE qq)
+ {
+- return sf_mathieu_eval(order, qq, gsl_sf_mathieu_a);
++ return sf_mathieu_eval(order, qq, gsl_sf_mathieu_a_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_a_array(VALUE module, int argc, VALUE *argv)
+ {
+@@ -145,11 +145,11 @@
+ }
+ static VALUE rb_gsl_sf_mathieu_b_e(VALUE module, VALUE order, VALUE qq)
+ {
+- return rb_gsl_sf_eval_e_int_double(gsl_sf_mathieu_b, order, qq);
++ return rb_gsl_sf_eval_e_int_double(gsl_sf_mathieu_b_e, order, qq);
+ }
+ static VALUE rb_gsl_sf_mathieu_b(VALUE module, VALUE order, VALUE qq)
+ {
+- return sf_mathieu_eval(order, qq, gsl_sf_mathieu_b);
++ return sf_mathieu_eval(order, qq, gsl_sf_mathieu_b_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_b_array(VALUE module, int argc, VALUE *argv)
+ {
+@@ -157,11 +157,11 @@
+ }
+ static VALUE rb_gsl_sf_mathieu_ce_e(VALUE module, VALUE order, VALUE qq, VALUE zz)
+ {
+- return sf_mathieu_eval_e_int_double2(order, qq, zz, gsl_sf_mathieu_ce);
++ return sf_mathieu_eval_e_int_double2(order, qq, zz, gsl_sf_mathieu_ce_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_ce(VALUE module, VALUE order, VALUE qq, VALUE zz)
+ {
+- return sf_mathieu_eval_int_double2(order, qq, zz, gsl_sf_mathieu_ce);
++ return sf_mathieu_eval_int_double2(order, qq, zz, gsl_sf_mathieu_ce_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_ce_array(VALUE module, int argc, VALUE *argv)
+ {
+@@ -169,11 +169,11 @@
+ }
+ static VALUE rb_gsl_sf_mathieu_se_e(VALUE module, VALUE order, VALUE qq, VALUE zz)
+ {
+- return sf_mathieu_eval_e_int_double2(order, qq, zz, gsl_sf_mathieu_se);
++ return sf_mathieu_eval_e_int_double2(order, qq, zz, gsl_sf_mathieu_se_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_se(VALUE module, VALUE order, VALUE qq, VALUE zz)
+ {
+- return sf_mathieu_eval_int_double2(order, qq, zz, gsl_sf_mathieu_se);
++ return sf_mathieu_eval_int_double2(order, qq, zz, gsl_sf_mathieu_se_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_se_array(VALUE module, int argc, VALUE *argv)
+ {
+@@ -183,11 +183,11 @@
+ /*****/
+ static VALUE rb_gsl_sf_mathieu_Mc_e(VALUE module, VALUE n1, VALUE n2, VALUE q, VALUE x)
+ {
+- return sf_mathieu_eval_e_int2_double2(n1, n2, q, x, gsl_sf_mathieu_Mc);
++ return sf_mathieu_eval_e_int2_double2(n1, n2, q, x, gsl_sf_mathieu_Mc_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_Mc(VALUE module, VALUE n1, VALUE n2, VALUE q, VALUE x)
+ {
+- return sf_mathieu_eval2(n1, n2, q, x, gsl_sf_mathieu_Mc);
++ return sf_mathieu_eval2(n1, n2, q, x, gsl_sf_mathieu_Mc_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_Mc_array(VALUE module, int argc, VALUE *argv)
+ {
+@@ -195,11 +195,11 @@
+ }
+ static VALUE rb_gsl_sf_mathieu_Ms_e(VALUE module, VALUE n1, VALUE n2, VALUE q, VALUE x)
+ {
+- return sf_mathieu_eval_e_int2_double2(n1, n2, q, x, gsl_sf_mathieu_Ms);
++ return sf_mathieu_eval_e_int2_double2(n1, n2, q, x, gsl_sf_mathieu_Ms_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_Ms(VALUE module, VALUE n1, VALUE n2, VALUE q, VALUE x)
+ {
+- return sf_mathieu_eval2(n1, n2, q, x, gsl_sf_mathieu_Ms);
++ return sf_mathieu_eval2(n1, n2, q, x, gsl_sf_mathieu_Ms_e);
+ }
+ static VALUE rb_gsl_sf_mathieu_Ms_array(VALUE module, int argc, VALUE *argv)
+ {
+--- a/ext/gsl_native/sf_ellint.c
++++ b/ext/gsl_native/sf_ellint.c
+@@ -82,17 +82,17 @@
+ static VALUE rb_gsl_sf_ellint_D(int argc, VALUE *argv, VALUE obj)
+ {
+ if (argc == 3)
+- return rb_gsl_sf_eval_double3_m(gsl_sf_ellint_D, argv[0], argv[1], argv[2],
++ return rb_gsl_sf_eval_double2_m(gsl_sf_ellint_D, argv[0], argv[1],
+ INT2FIX(GSL_PREC_DOUBLE));
+ else
+- return rb_gsl_sf_eval_double3_m(gsl_sf_ellint_D, argv[0], argv[1], argv[2],
++ return rb_gsl_sf_eval_double2_m(gsl_sf_ellint_D, argv[0], argv[1],
+ argv[3]);
+ }
+
+ static VALUE rb_gsl_sf_ellint_D_e(VALUE obj, VALUE phi, VALUE k,
+- VALUE n, VALUE m)
++ VALUE m)
+ {
+- return rb_gsl_sf_eval_e_double3_m(gsl_sf_ellint_D_e, phi, k, n, m);
++ return rb_gsl_sf_eval_e_double2_m(gsl_sf_ellint_D_e, phi, k, m);
+ }
+
+ static VALUE rb_gsl_sf_ellint_RC(int argc, VALUE *argv, VALUE obj)
diff --git a/debian/patches/gsl2_tamu_anova.patch b/debian/patches/gsl2_tamu_anova.patch
new file mode 100644
index 0000000..7185dae
--- /dev/null
+++ b/debian/patches/gsl2_tamu_anova.patch
@@ -0,0 +1,20 @@
+Description: fix compiler warning about pointer passed instead of its value
+Author: Cédric Boutillier <boutil at debian.org>
+Origin: vendor
+Bug-Debian: https://bugs.debian.org/804499
+Bug: https://github.com/SciRuby/rb-gsl/issues/24
+Forwarded: https://github.com/SciRuby/rb-gsl/pull/31
+Last-Update: 2016-02-29
+
+--- a/ext/gsl_native/tamu_anova.c
++++ b/ext/gsl_native/tamu_anova.c
+@@ -32,7 +32,7 @@
+ VALUE rb_tamu_anova_printtable(VALUE *vTable)
+ {
+ struct tamu_anova_table *table;
+- Data_Get_Struct(vTable, struct tamu_anova_table, table);
++ Data_Get_Struct(*vTable, struct tamu_anova_table, table);
+ tamu_anova_printtable(*table);
+ return Qtrue;
+ }
+
diff --git a/debian/patches/series b/debian/patches/series
index 46e5b7d..b7d1464 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,4 @@
20110605_extconf.rb
+gsl2_multifit.patch
+gsl2_special_functions.patch
+gsl2_tamu_anova.patch
--
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