From 71deace00d1a2b091313fe137ab7092418c6f87c Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 10 Feb 2020 21:05:55 +0000
Subject: gentoo resync : 10.02.2020

---
 sci-chemistry/autodock_vina/Manifest               |  3 ++-
 .../autodock_vina/autodock_vina-1.1.2.ebuild       | 29 ++++++++++++----------
 .../autodock_vina-1.1.2-missing-debug-decl.patch   | 11 ++++++++
 3 files changed, 29 insertions(+), 14 deletions(-)
 create mode 100644 sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch

(limited to 'sci-chemistry/autodock_vina')

diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index b727a4092ac8..68deb91152ce 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1,5 +1,6 @@
 AUX 1.1.2-gentoo.patch 2448 BLAKE2B f63add1d0fec8716672672af78fe8f34053bf060044e78fcf30ca6054e4075a5f12ac3a903812c9cd619dc34fa854603c8369c8acfcf17130d1b24b50b3d5373 SHA512 d8165d88f3e91064c74f1506a7f58473a74f6ebf993165827694d78170b29227dc378c61a7f096a3c49708b713583aca3d5714827d1fe43a5bb37f3d648d2613
 AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 BLAKE2B 70c55e95e9728221ba80177989fde0cc6c93b479779aa0dda45dcad79b97018fe934ea56b4ede4af20ce867b6ed39c3958a5529b8f286aec33ec7ea53d339ada SHA512 4226fb0d7196362a02afa4e0b0616146ef816a439dd63e1bffbfef183975fe7e6260318f919e9d9835d2d47973542b5340e93ad35b070467e42c0990f9a635f7
+AUX autodock_vina-1.1.2-missing-debug-decl.patch 365 BLAKE2B 959b46facdce27850a1f9fd6c66ecc297e4ad089e79896b9fe2127e425bd1bfcfce5d676cf2e4336c47d3a72b0e8319c791fdf1a5807f244cf5b4528de8cbb25 SHA512 ddbdca76fca16b46fd042b57eb941b7ba67f59f46c35dc18428ea6873c8ed5f03051247b8c667a08af8de40fccb0caf851848bb9082536225cacf8eb3e313c98
 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9
-EBUILD autodock_vina-1.1.2.ebuild 932 BLAKE2B 57b02ce051bada78490a4c335f6b10d380ce900dad66c5f3228aea927d7e1814baecf357b080683df87e26ae15ab2c3b97cc3f3ceb7e93502f67e8a834257190 SHA512 39f8acb795d17786a5112a4e70bf67c6ab594d25ab5eb4b739e2b0c70a9e0548265bcd5f36b6d4915b82b43a0f463187f8d9dc5aaa62f925c5172950a6bc26ee
+EBUILD autodock_vina-1.1.2.ebuild 945 BLAKE2B 034a455deebf74c3f5170e5fd33eb30f4a2f8d5668af864d28dd0835c9a4a17367077c16c507ba5d798a2dbcb1b6d6b6f74f4de27a2b5869ef175100f0a732f8 SHA512 8174a0431930d8f591bf03601ea67b0bdf720a6d2fe102f4eda2e5d10f68c36166ae051abdd46dc2b4355213472c85da79d60d50f7ff1e7e2dd05683e06525a1
 MISC metadata.xml 1244 BLAKE2B 7df9f6f260c038c4f6b02a9fe35b54dbdc165975373ece6fb27856893536b3af7218ca1ff487ba908caa8c9beea43dc3f503fc83b6cf685754b8f17e53d771a9 SHA512 121a82bab7f4126fe5afe4ad39bbc9e397483c485e8a5771129d8eff883e87248acb1d689d47a57bf792ea8e1e23e82dec9bde811dae44e9b86a6736944c3484
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
index bbff27f85e2f..59f14e8086c9 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -1,40 +1,43 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils flag-o-matic versionator
+inherit flag-o-matic
 
-MY_P="${PN}_$(replace_all_version_separators _)"
+MY_P="${PN}_$(ver_rs 1- _)"
 
 DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
 HOMEPAGE="http://vina.scripps.edu/"
 SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz"
 
+LICENSE="Apache-2.0"
 SLOT="0"
 KEYWORDS="amd64 x86"
-LICENSE="Apache-2.0"
 IUSE="debug"
 
-RDEPEND="dev-libs/boost[threads]"
+RDEPEND="dev-libs/boost:=[threads]"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/${MY_P}/build/linux/release
 
+PATCHES=(
+	"${FILESDIR}"/${PV}-gentoo.patch
+	"${FILESDIR}"/${P}-boost-filesystem.patch
+	"${FILESDIR}"/${P}-missing-debug-decl.patch
+)
+
 src_prepare() {
 	cd "${WORKDIR}"/${MY_P} || die
-	epatch \
-		"${FILESDIR}"/${PV}-gentoo.patch \
-		"${FILESDIR}"/${P}-boost-filesystem.patch
+	default
 }
 
-src_compile() {
-	local c_options
-
+src_configure() {
 	use debug || c_options="-DNDEBUG"
-
 	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3
+}
 
+src_compile() {
 	emake \
 		BASE="${EPREFIX}"/usr/ \
 		GPP="$(tc-getCXX)" \
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch
new file mode 100644
index 000000000000..c68adb1bff21
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch
@@ -0,0 +1,11 @@
+--- a/src/lib/quaternion.h
++++ b/src/lib/quaternion.h
+@@ -70,6 +70,8 @@
+ 	return sqr(q.R_component_1()) + sqr(q.R_component_2()) + sqr(q.R_component_3()) + sqr(q.R_component_4());
+ }
+ 
++bool quaternion_is_normalized(const qt& q);
++
+ inline void quaternion_normalize(qt& q) {
+ 	const fl s = quaternion_norm_sqr(q);
+ 	assert(eq(s, sqr(boost::math::abs(q))));
-- 
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