sci-libs/cctbx: Add fix for gcc-4.7

Package-Manager: portage-2.2.0_alpha110/cvs/Linux x86_64

4 files changed, 176 insertions, 5 deletions

diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
index e95a969cc7b5..82c608a7826b 100644
--- a/sci-libs/cctbx/ChangeLog
+++ b/sci-libs/cctbx/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-libs/cctbx
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.25 2012/06/14 18:44:19 jdhore Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.26 2012/06/19 14:59:00 jlec Exp $
+
+  19 Jun 2012; Justin Lecher <jlec@gentoo.org>
+  +files/2010.03.29.2334-gcc-4.7.patch, cctbx-2010.03.29.2334-r6.ebuild:
+  Add fix for gcc-4.7
 
   14 Jun 2012; Jeff Horelick <jdhore@gentoo.org>
   cctbx-2010.03.29.2334-r6.ebuild:
diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest
index 5b3e13f588fd..e1bde6e4eef9 100644
--- a/sci-libs/cctbx/Manifest
+++ b/sci-libs/cctbx/Manifest
@@ -1,13 +1,25 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX 2010.03.29.2334-boost.patch 18175 RMD160 cf972e6d792d98d152eb18453f0349c87efbbb97 SHA1 f9dac88aea0e898259537a343650cbcd53b6f01f SHA256 f6a8a246dfd42e7981687802a0e00d933759d3c749c0344bfbfbfde12814f4d7
 AUX 2010.03.29.2334-clipper.patch 2209 RMD160 1bfc13f0834e837a55f0e41554649acd1e45b80c SHA1 a81ee2cc94805b6ef1e609c2ea402a1c9f429d62 SHA256 e7c8bf813bedd3b67de5ce727d5f75e9635568769373f237e7b624ed143351b1
 AUX 2010.03.29.2334-flags.patch 3336 RMD160 fdbb0b71499e00c666629e1ff04b5bdcbe376b13 SHA1 ef97099dbd93727bd356015f22e82480a48e1a0c SHA256 769edb3e5dcb608b54ab4d33c5933b523f73ff62c6cb627c4eb4b1a2086e40b1
 AUX 2010.03.29.2334-gcc-4.6.patch 1059 RMD160 c999a541a0164438c13d5b9da5e00476fd37df03 SHA1 e4a5c60493d74a9c102aea4cc9d5607fc10fc526 SHA256 dad06be10e1ba3fefee9f9aa79a897635cb8362f5719c5c8c5e5c25d1bea6236
+AUX 2010.03.29.2334-gcc-4.7.patch 6747 RMD160 7124c760a6770c4c32e0030b90e607f049cd8ba3 SHA1 2d4e468babf685f6ec2128ceeffa457c5743f236 SHA256 ab01875a97ece09e4d729bb435b67960eff6193c27454cc889f0dda0cd3c92a5
 AUX 2010.03.29.2334-soname.patch 5177 RMD160 c6cad498c4edb7046696428008408b126efa954c SHA1 7c5d78110c4270c9ca113ae5ea77c7c2451e2b21 SHA256 dd4ea6dbf34c1b2d9572adec5a33fe6a73b1a99e8c4364123e69382bb161ce74
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 DIST cctbx-2010.03.29.2334.tar.gz 15570372 RMD160 e543578dbe6568f5f8f80b3ce7a20b10e01193bc SHA1 1442dbd5d1ef3b91e718dce039a24fc1637104d3 SHA256 e1fae804caaf8593c7a3f32e4544046f4c00293063d9099721578cc8fbd17213
 EBUILD cctbx-2010.03.29.2334-r3.ebuild 6038 RMD160 aeb88302efeacb9711f5dece8c2865292f64ba35 SHA1 3b1c16e35b244816faed1b7db8ff71859aec8867 SHA256 34e695fe1e4a93389f5753f425fd09deddc66796981061ee689f1ddd56caec72
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diff --git a/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild
index c0b42a55a099..ab3064ce2bc1 100644
--- a/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild
+++ b/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild,v 1.4 2012/06/14 18:44:19 jdhore Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r6.ebuild,v 1.5 2012/06/19 14:59:00 jlec Exp $
 
 EAPI="3"
 
@@ -55,7 +55,8 @@ src_prepare() {
 		"${FILESDIR}"/${PV}-clipper.patch \
 		"${FILESDIR}"/${PV}-flags.patch \
 		"${FILESDIR}"/${PV}-soname.patch \
-		"${FILESDIR}"/${PV}-gcc-4.6.patch
+		"${FILESDIR}"/${PV}-gcc-4.6.patch \
+		"${FILESDIR}"/${PV}-gcc-4.7.patch
 
 	eprefixify "${MY_S}"/scitbx/libtbx_refresh.py
 
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch
new file mode 100644
index 000000000000..96cb21531bbf
--- /dev/null
+++ b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch
@@ -0,0 +1,154 @@
+ .../scitbx/math/boost_python/distributions.cpp     |   60 +++++++++++++------
+ cctbx_sources/scitbx/rigid_body/spatial_lib.h      |    1 +
+ cctbx_sources/scitbx/rigid_body/tardy.h            |    4 +-
+ .../refinement/boost_python/weighting_schemes.cpp  |    4 +-
+ .../smtbx/structure_factors/direct/standard_xray.h |    4 +-
+ 5 files changed, 48 insertions(+), 25 deletions(-)
+
+diff --git a/cctbx_sources/scitbx/math/boost_python/distributions.cpp b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
+index a676798..68818e7 100644
+--- a/cctbx_sources/scitbx/math/boost_python/distributions.cpp
++++ b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
+@@ -59,29 +59,51 @@ namespace {
+   {
+     typedef Distribution wt;
+ 
++    #define NEW_MEMBER(name)                \
++    static FloatType name(wt const &self) { \
++      return boost::math::name(self);                    \
++    }
++
++    NEW_MEMBER(mean);
++    NEW_MEMBER(median);
++    NEW_MEMBER(mode);
++    NEW_MEMBER(variance);
++    NEW_MEMBER(standard_deviation);
++    NEW_MEMBER(skewness);
++    NEW_MEMBER(kurtosis);
++
++    #undef NEW_MEMBER
++
++    #define NEW_MEMBER(name)                               \
++    static FloatType name(wt const &self, FloatType arg) { \
++      return boost::math::name(self, arg);                              \
++    }
++
++    NEW_MEMBER(pdf);
++    NEW_MEMBER(cdf);
++    NEW_MEMBER(quantile);
++
++    #undef NEW_MEMBER
++
++    static scitbx::af::shared<FloatType> quantiles(wt const &self, std::size_t n) {
++      return scitbx::math::quantiles<FloatType>(self, n);
++    }
++
+     static void
+     wrap()
+     {
+       using namespace boost::python;
+-      def("mean", (FloatType(*)(wt const&)) boost::math::mean);
+-      def("median", (FloatType(*)(wt const&)) boost::math::median);
+-      def("mode", (FloatType(*)(wt const&)) boost::math::mode);
+-      def("variance", (FloatType(*)(wt const&)) boost::math::variance);
+-      def("standard_deviation",
+-        (FloatType(*)(wt const&)) boost::math::standard_deviation);
+-      def("skewness", (FloatType(*)(wt const&)) boost::math::skewness);
+-      def("kurtosis", (FloatType(*)(wt const&)) boost::math::kurtosis);
+-      def("pdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::pdf);
+-      def("cdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::cdf);
+-      def("quantile", (FloatType(*)(wt const&, FloatType const&))
+-        boost::math::quantile);
+-      def("quantiles",
+-#if BOOST_WORKAROUND(__EDG_VERSION__, BOOST_TESTED_AT(306))
+-        (scitbx::af::shared<FloatType>(*)(wt const&, std::size_t)) quantiles
+-#else
+-        quantiles<FloatType, wt>
+-#endif
+-        );
++      def("mean"              , mean);
++      def("median"            , median);
++      def("mode"              , mode);
++      def("variance"          , variance);
++      def("standard_deviation", standard_deviation);
++      def("skewness"          , skewness);
++      def("kurtosis"          , kurtosis);
++      def("pdf"               , pdf);
++      def("cdf"               , cdf);
++      def("quantile"          , quantile);
++      def("quantiles"         , quantiles);
+     }
+   };
+ 
+diff --git a/cctbx_sources/scitbx/rigid_body/spatial_lib.h b/cctbx_sources/scitbx/rigid_body/spatial_lib.h
+index a084f0f..e377292 100755
+--- a/cctbx_sources/scitbx/rigid_body/spatial_lib.h
++++ b/cctbx_sources/scitbx/rigid_body/spatial_lib.h
+@@ -2,6 +2,7 @@
+ #define SCITBX_RIGID_BODY_SPATIAL_LIB_H
+ 
+ #include <scitbx/rotr3.h>
++#include <scitbx/rigid_body/matrix_helpers.h>
+ #include <scitbx/array_family/versa_matrix.h>
+ 
+ namespace scitbx { namespace rigid_body {
+diff --git a/cctbx_sources/scitbx/rigid_body/tardy.h b/cctbx_sources/scitbx/rigid_body/tardy.h
+index 104f16b..a8f76cc 100755
+--- a/cctbx_sources/scitbx/rigid_body/tardy.h
++++ b/cctbx_sources/scitbx/rigid_body/tardy.h
+@@ -346,7 +346,7 @@ namespace tardy {
+       unsigned nb = this->bodies_size();
+       af::shared<af::small<ft, 7> > result((af::reserve(nb)));
+       af::shared<af::small<ft, 6> >
+-        tau_array = f_ext_as_tau(f_ext_array().const_ref());
++        tau_array = this->f_ext_as_tau(f_ext_array().const_ref());
+       for(unsigned ib=0;ib<nb;ib++) {
+         result.push_back(
+           this->bodies[ib]->joint->tau_as_d_e_pot_d_q(tau_array[ib]));
+@@ -379,7 +379,7 @@ namespace tardy {
+     qdd_array()
+     {
+       if (!qdd_array_) {
+-        qdd_array_ = forward_dynamics_ab(
++        qdd_array_ = this->forward_dynamics_ab(
+           /*tau_array*/ af::const_ref<af::small<ft, 6> >(0, 0),
+           f_ext_array().const_ref(),
+           /*grav_accn*/ af::const_ref<ft>(0, 0));
+diff --git a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
+index ce0c27b..904e8d7 100644
+--- a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
++++ b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
+@@ -25,9 +25,9 @@ namespace smtbx { namespace refinement { namespace least_squares {
+       : base_t(name, boost::python::no_init)
+     {
+       using namespace boost::python;
+-      def("__call__", &wt::operator(),
++      this->def("__call__", &wt::operator(),
+           (arg("fo_sq"), arg("sigma"), arg("fc_sq")));
+-      def("__call__", weights,
++      this->def("__call__", weights,
+           (arg("fo_sq"), arg("sigmas"), arg("fc_sq")));
+     }
+   };
+diff --git a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
+index 5e2df76..911bfde 100644
+--- a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
++++ b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
+@@ -161,7 +161,7 @@ namespace smtbx { namespace structure_factors { namespace direct {
+         for (int k=0; k < hr_ht.groups.size(); ++k) {
+           hr_ht_group<float_type> const &g = hr_ht.groups[k];
+           float_type hrx = g.hr * scatterer.site;
+-          complex_type f = exp_i_2pi(hrx + g.ht);
++          complex_type f = this->exp_i_2pi(hrx + g.ht);
+           if (scatterer.flags.use_u_aniso()) {
+             float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star);
+             f *= dw;
+@@ -336,7 +336,7 @@ namespace smtbx { namespace structure_factors { namespace direct {
+         for (int k=0; k < hr_ht.groups.size(); ++k) {
+           hr_ht_group<float_type> const &g = hr_ht.groups[k];
+           float_type hrx = g.hr * scatterer.site;
+-          complex_type f = exp_i_2pi(hrx + g.ht);
++          complex_type f = this->exp_i_2pi(hrx + g.ht);
+           float_type fa = f.real(), fb = f.imag();
+           if (scatterer.flags.use_u_aniso()) {
+             float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star);