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authorDavid Seifert <soap@gentoo.org>2017-09-16 15:52:10 +0200
committerDavid Seifert <soap@gentoo.org>2017-09-16 15:59:08 +0200
commitc088dec53c87470f6eb3e6afd62801f5017fb914 (patch)
tree8c92da7c227ea82e94f61b4965c99c4484aa9533 /sci-chemistry/dssp
parentnet-analyzer/tcpdump: Restore stable 4.9.2 for amd64 and x86 (diff)
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sci-chemistry/dssp: Fix boost TR1 header include
Closes: https://bugs.gentoo.org/630776 Package-Manager: Portage-2.3.8, Repoman-2.3.3
Diffstat (limited to 'sci-chemistry/dssp')
-rw-r--r--sci-chemistry/dssp/dssp-2.2.1-r1.ebuild28
-rw-r--r--sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch82
2 files changed, 97 insertions, 13 deletions
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
index a50e602ad32b..b660e9ef3c96 100644
--- a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
+++ b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
-inherit eutils multilib toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="The protein secondary structure standard"
HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/"
@@ -17,17 +17,19 @@ IUSE=""
RDEPEND="dev-libs/boost:=[threads]"
DEPEND="${RDEPEND}"
-src_prepare() {
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.1.0-gentoo.patch
+ "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch
+)
+
+src_configure() {
tc-export CXX
- cat >> make.config <<- EOF
- BOOST_LIB_SUFFIX = -mt
- BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)"
- BOOST_INC_DIR = "${EPREFIX}/usr/include"
+ cat >> make.config <<- EOF || die
+ BOOST_LIB_SUFFIX = -mt
+ BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)"
+ BOOST_INC_DIR = "${EPREFIX}/usr/include"
EOF
-
- epatch \
- "${FILESDIR}"/${PN}-2.1.0-gentoo.patch
}
src_install() {
@@ -36,8 +38,8 @@ src_install() {
doman doc/mkdssp.1
dodoc README.txt changelog
- cat >> "${T}"/30-${PN} <<- EOF
- DSSP="${EPREFIX}"/usr/bin/${PN}
+ cat >> "${T}"/30-${PN} <<- EOF || die
+ DSSP="${EPREFIX}"/usr/bin/${PN}
EOF
doenvd "${T}"/30-${PN}
}
diff --git a/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch b/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch
new file mode 100644
index 000000000000..4eee6b567349
--- /dev/null
+++ b/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch
@@ -0,0 +1,82 @@
+--- a/src/dssp.cpp
++++ b/src/dssp.cpp
+@@ -73,7 +73,7 @@
+
+ double alpha;
+ char chirality;
+- tr1::tie(alpha,chirality) = residue.Alpha();
++ boost::tie(alpha,chirality) = residue.Alpha();
+
+ uint32 bp[2] = {};
+ char bridgelabel[2] = { ' ', ' ' };
+--- a/src/primitives-3d.cpp
++++ b/src/primitives-3d.cpp
+@@ -153,7 +153,7 @@
+
+ // --------------------------------------------------------------------
+
+-tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
++boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
+ {
+ if (q.R_component_1() > 1)
+ q = Normalize(q);
+@@ -169,7 +169,7 @@
+
+ MPoint axis(q.R_component_2() / s, q.R_component_3() / s, q.R_component_4() / s);
+
+- return tr1::make_tuple(angle, axis);
++ return boost::make_tuple(angle, axis);
+ }
+
+ MPoint CenterPoints(vector<MPoint>& points)
+--- a/src/primitives-3d.h
++++ b/src/primitives-3d.h
+@@ -9,7 +9,7 @@
+
+ #include <vector>
+
+-#include <boost/tr1/tuple.hpp>
++#include <boost/tuple/tuple.hpp>
+ #include <boost/math/quaternion.hpp>
+
+ typedef boost::math::quaternion<double> MQuaternion;
+@@ -64,7 +64,7 @@
+
+ MQuaternion Normalize(MQuaternion q);
+
+-std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
++boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
+ MPoint Centroid(std::vector<MPoint>& points);
+ MPoint CenterPoints(std::vector<MPoint>& points);
+ MQuaternion AlignPoints(const std::vector<MPoint>& a, const std::vector<MPoint>& b);
+--- a/src/structure.cpp
++++ b/src/structure.cpp
+@@ -544,7 +544,7 @@
+ return result;
+ }
+
+-tr1::tuple<double,char> MResidue::Alpha() const
++boost::tuple<double,char> MResidue::Alpha() const
+ {
+ double alhpa = 360;
+ char chirality = ' ';
+@@ -558,7 +558,7 @@
+ else
+ chirality = '+';
+ }
+- return tr1::make_tuple(alhpa, chirality);
++ return boost::make_tuple(alhpa, chirality);
+ }
+
+ double MResidue::Kappa() const
+--- a/src/structure.h
++++ b/src/structure.h
+@@ -168,7 +168,7 @@
+
+ double Phi() const;
+ double Psi() const;
+- std::tr1::tuple<double,char>
++ boost::tuple<double,char>
+ Alpha() const;
+ double Kappa() const;
+ double TCO() const;