[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/autodock_vina/, sci-chemistry/autodock_vina/files/

[David Seifert]

commit:     bbc280302422f9a4e29bc5867894f415d8a3ec0d
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb  8 10:55:49 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb  8 10:55:49 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bbc28030

sci-chemistry/autodock_vina: Port to EAPI 7

Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 .../autodock_vina/autodock_vina-1.1.2.ebuild       | 29 ++++++++++++----------
 .../autodock_vina-1.1.2-missing-debug-decl.patch   | 11 ++++++++
 2 files changed, 27 insertions(+), 13 deletions(-)

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 bbff27f85e2..59f14e8086c 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 00000000000..c68adb1bff2
--- /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))));