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

2024-07-12 Thread Arthur Zamarin 
commit: f5b9787ed57d24652fe4a8dc8401d35bd78c7b99
Author: Arthur Zamarin  gentoo  org>
AuthorDate: Sat Jul 13 05:22:16 2024 +
Commit: Arthur Zamarin  gentoo  org>
CommitDate: Sat Jul 13 05:22:16 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f5b9787e

sci-chemistry/autodock_vina: Stabilize 1.2.5 amd64, #935909

Signed-off-by: Arthur Zamarin  gentoo.org>

 sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild 
b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
index a74066d3963a..dd396732c357 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
@@ -15,7 +15,7 @@ S="${WORKDIR}/${MY_PN}-${PV}/build/linux/release"
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
 IUSE="debug"
 
 RDEPEND="dev-libs/boost:="

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

2024-07-12 Thread Sam James 
commit: e7ea26f08a0d2a9b4c4f4c385a8c2488c073387c
Author: Sam James  gentoo  org>
AuthorDate: Fri Jul 12 20:17:28 2024 +
Commit: Sam James  gentoo  org>
CommitDate: Fri Jul 12 20:17:28 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e7ea26f0

sci-chemistry/autodock_vina: fix build w/ boost-1.85

Closes: https://bugs.gentoo.org/932237
Signed-off-by: Sam James  gentoo.org>

 .../autodock_vina/autodock_vina-1.2.5.ebuild|  1 +
 .../files/autodock_vina-1.2.5-boost-1.85.patch  | 21 +
 2 files changed, 22 insertions(+)

diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild 
b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
index e9edf1f9c991..a74066d3963a 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
@@ -23,6 +23,7 @@ DEPEND="${RDEPEND}"
 
 PATCHES=(
"${FILESDIR}"/${P}-gentoo.patch
+   "${FILESDIR}"/${P}-boost-1.85.patch
 )
 
 src_prepare() {

diff --git 
a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch 
b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch
new file mode 100644
index ..55906b093a49
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch
@@ -0,0 +1,21 @@
+https://bugs.gentoo.org/932237
+--- a/src/lib/vina.h
 b/src/lib/vina.h
+@@ -35,7 +35,6 @@
+ #include 
+ #include 
+ #include 
+-#include  // filesystem::basename
+ #include  // hardware_concurrency // FIXME rm ?
+ #include 
+ //#include 
+--- a/src/split/split.cpp
 b/src/split/split.cpp
+@@ -30,7 +30,6 @@
+ #include 
+ #include 
+ #include 
+-#include  // filesystem::basename
+ 
+ #include "file.h"
+ #include "parse_error.h"

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

2024-03-26 Thread Alexey Shvetsov 
commit: e946f4c6951ed2ea86b806b3bef37b8c5ba7af01
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Tue Mar  5 10:57:33 2024 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Tue Mar 26 10:53:17 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e946f4c6

sci-chemistry/autodock_vina: add github upstream metadata

Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/autodock_vina/metadata.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sci-chemistry/autodock_vina/metadata.xml 
b/sci-chemistry/autodock_vina/metadata.xml
index f29cb87a5701..ec0a09453889 100644
--- a/sci-chemistry/autodock_vina/metadata.xml
+++ b/sci-chemistry/autodock_vina/metadata.xml
@@ -17,4 +17,7 @@
multithreading
Journal of Computational Chemistry 31 (2010) 455-461

+   
+   ccsb-scripps/AutoDock-Vina
+

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

2024-03-26 Thread Alexey Shvetsov 
commit: c2eae57dd0815a47e8c59e0c6dbcda1eea67f949
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Tue Mar  5 10:56:54 2024 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Tue Mar 26 10:53:06 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c2eae57d

sci-chemistry/autodock_vina: add 1.2.5

Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/autodock_vina/Manifest   |  1 +
 .../autodock_vina/autodock_vina-1.2.5.ebuild   | 50 +
 .../files/autodock_vina-1.2.5-gentoo.patch | 64 ++
 3 files changed, 115 insertions(+)

diff --git a/sci-chemistry/autodock_vina/Manifest 
b/sci-chemistry/autodock_vina/Manifest
index 67f2032d2856..e4088c449178 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1 +1,2 @@
+DIST autodock_vina-1.2.5.tar.gz 24158966 BLAKE2B 
c11493fcb35d409b97f639c4da48967d5df450781d412d80a951b95162555f4b1dfba809a01062136a7f0664c0b9a01a42b5403ee1d278a57afd669cf1f96321
 SHA512 
d36908e5833d22bcbc4dae353ef32b905d6eb46511302f7583a291398bfadff5e75fc99ce7b380860578b2257e5c32434cc75b1ca51fafb4b5f12d9477a878e9
 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B 
dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c
 SHA512 
f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9

diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild 
b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
new file mode 100644
index ..e9edf1f9c991
--- /dev/null
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PN=AutoDock-Vina
+
+DESCRIPTION="Program for drug discovery, molecular docking and virtual 
screening"
+HOMEPAGE="http://vina.scripps.edu/";
+SRC_URI="https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v${PV}.tar.gz
 -> ${P}.tar.gz"
+
+S="${WORKDIR}/${MY_PN}-${PV}/build/linux/release"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug"
+
+RDEPEND="dev-libs/boost:="
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+   "${FILESDIR}"/${P}-gentoo.patch
+)
+
+src_prepare() {
+   cd "${WORKDIR}/${MY_PN}-${PV}" || die
+   pwd
+   sed -e "s:VERSION:\"${PV}\":g" \
+   -i src/main/main.cpp \
+   -i src/split/split.cpp || die
+   default
+}
+
+src_configure() {
+   append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 
-DBOOST_TIMER_ENABLE_DEPRECATED -std=c++14
+}
+
+src_compile() {
+   emake \
+   BASE="${EPREFIX}"/usr/ \
+   GPP="$(tc-getCXX)" \
+   C_OPTIONS=$(usex debug '' -DNDEBUG)
+}
+
+src_install() {
+   dobin vina{,_split}
+}

diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch 
b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch
new file mode 100644
index ..e7bf1d5007ff
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch
@@ -0,0 +1,64 @@
+diff -urN AutoDock-Vina-1.2.5.orig/build/linux/debug/Makefile 
AutoDock-Vina-1.2.5/build/linux/debug/Makefile
+--- AutoDock-Vina-1.2.5.orig/build/linux/debug/Makefile2024-03-05 
13:23:49.210511903 +0300
 AutoDock-Vina-1.2.5/build/linux/debug/Makefile 2024-03-05 
13:25:34.028499976 +0300
+@@ -1,7 +1,7 @@
+ BASE=/usr
+ BOOST_VERSION=
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=g++
+ C_OPTIONS= -g -std=gnu++11
+ BOOST_LIB_VERSION=
+diff -urN AutoDock-Vina-1.2.5.orig/build/linux/release/Makefile 
AutoDock-Vina-1.2.5/build/linux/release/Makefile
+--- AutoDock-Vina-1.2.5.orig/build/linux/release/Makefile  2024-03-05 
13:23:49.213845279 +0300
 AutoDock-Vina-1.2.5/build/linux/release/Makefile   2024-03-05 
13:26:10.285621339 +0300
+@@ -1,7 +1,7 @@
+ BASE=/usr/local
+ BOOST_VERSION=
+ BOOST_INCLUDE = $(BASE)/include
+-C_PLATFORM=-static -pthread
++C_PLATFORM=-pthread
+ GPP=g++
+ C_OPTIONS= -O3 -DNDEBUG -std=c++11
+ BOOST_LIB_VERSION=
+diff -urN AutoDock-Vina-1.2.5.orig/build/makefile_common 
AutoDock-Vina-1.2.5/build/makefile_common
+--- AutoDock-Vina-1.2.5.orig/build/makefile_common 2024-03-05 
13:23:49.213845279 +0300
 AutoDock-Vina-1.2.5/build/makefile_common  2024-03-05 13:28:30.557370911 
+0300
+@@ -14,7 +14,7 @@
+ #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} 
$(INCFLAGS)
+ CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+ 
+-LDFLAGS = -L$(BASE)/lib -L.
++LDFLAGS = -L.
+ 
+ # test if boost_thread-mt exists, this is
+ # necessary as some versions of boost only
+@@ -32,22 +32,22 @@
+ ifeq ($(BOOST_STATIC), y)
+ LIBS = ${BASE}/lib/libboost_system${BOOST_LIB_VERSION}.a 
${

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

2024-03-02 Thread Alexey Shvetsov 
commit: 8ff06565cfa9e2d6114008541f2fae2c23f9e12c
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Sat Mar  2 21:14:38 2024 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Sat Mar  2 21:14:38 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ff06565

sci-chemistry/autodock_vina: Fix build with recent boost

Closes: https://bugs.gentoo.org/913037
Closes: https://bugs.gentoo.org/924622
Signed-off-by: Alexey Shvetsov  gentoo.org>

 sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild 
b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
index a6495591339a..63810da09284 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -33,7 +33,7 @@ src_prepare() {
 }
 
 src_configure() {
-   append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -std=c++11
+   append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 
-DBOOST_TIMER_ENABLE_DEPRECATED -std=c++14
 }
 
 src_compile() {

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

2022-09-04 Thread David Seifert 
commit: 065341128da7f5a3d89dab94c1fc4c92ef7cb1ea
Author: David Seifert  gentoo  org>
AuthorDate: Sun Sep  4 12:22:28 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Sep  4 12:22:28 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06534112

sci-chemistry/autodock_vina: remove boost[threads(+)] usedep

Signed-off-by: David Seifert  gentoo.org>

 sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild 
b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
index a1782463270a..5e1ce226e6a7 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -16,7 +16,7 @@ SLOT="0"
 KEYWORDS="amd64 x86"
 IUSE="debug"
 
-RDEPEND="dev-libs/boost:=[threads(+)]"
+RDEPEND="dev-libs/boost:="
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/${MY_P}/build/linux/release

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

2022-01-08 Thread David Seifert 
commit: 4f6e0e4795d857ac2464334ec627a3856021ab44
Author: David Seifert  gentoo  org>
AuthorDate: Sat Jan  8 13:16:04 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Jan  8 13:16:04 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4f6e0e47

sci-chemistry/autodock_vina: remove useless  description

Signed-off-by: David Seifert  gentoo.org>

 sci-chemistry/autodock_vina/metadata.xml | 7 ---
 1 file changed, 7 deletions(-)

diff --git a/sci-chemistry/autodock_vina/metadata.xml 
b/sci-chemistry/autodock_vina/metadata.xml
index f603fd62c191..f29cb87a5701 100644
--- a/sci-chemistry/autodock_vina/metadata.xml
+++ b/sci-chemistry/autodock_vina/metadata.xml
@@ -17,11 +17,4 @@
multithreading
Journal of Computational Chemistry 31 (2010) 455-461

-

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

2021-06-18 Thread David Seifert 
commit: c3f45d09f47f9f2438f0ba723920b31927c35dae
Author: David Seifert  gentoo  org>
AuthorDate: Fri Jun 18 19:17:23 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Jun 18 19:17:23 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c3f45d09

sci-chemistry/autodock_vina: Depend on dev-libs/boost:=[threads(+)]

Package-Manager: Portage-3.0.20, Repoman-3.0.3
Signed-off-by: David Seifert  gentoo.org>

 .../{autodock_vina-1.1.2.ebuild => autodock_vina-1.1.2-r1.ebuild}   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild 
b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
similarity index 95%
rename from sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
rename to sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
index 19a6a106be7..a1782463270 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
 KEYWORDS="amd64 x86"
 IUSE="debug"
 
-RDEPEND="dev-libs/boost:=[threads]"
+RDEPEND="dev-libs/boost:=[threads(+)]"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/${MY_P}/build/linux/release

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

2021-05-16 Thread Andreas Sturmlechner 
commit: 94ad7eb2a2a84490626fe423556e8c15bb93a8b6
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sun May 16 17:34:33 2021 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun May 16 17:34:50 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=94ad7eb2

sci-chemistry/autodock_vina: Fix build w/ boost-1.69

Closes: https://bugs.gentoo.org/789702
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild | 7 +++
 1 file changed, 3 insertions(+), 4 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 354d80938d4..19a6a106be7 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -33,15 +33,14 @@ src_prepare() {
 }
 
 src_configure() {
-   use debug || c_options="-DNDEBUG"
-   append-cxxflags -DBOOST_FILESYSTEM_VERSION=3
+   append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -std=c++11
 }
 
 src_compile() {
emake \
BASE="${EPREFIX}"/usr/ \
GPP="$(tc-getCXX)" \
-   C_OPTIONS="${c_options}"
+   C_OPTIONS=$(usex debug '' -DNDEBUG)
 }
 
 src_install() {

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

2020-02-08 Thread David Seifert 
commit: bbc280302422f9a4e29bc5867894f415d8a3ec0d
Author: David Seifert  gentoo  org>
AuthorDate: Sat Feb  8 10:55:49 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Feb  8 10:55:49 2020 +
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  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 000..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;

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

2015-08-16 Thread Justin Lecher 
commit: 1736183b6d7f2f753c9b275bd1d7085e0549705f
Author: Justin Lecher  gentoo  org>
AuthorDate: Sun Aug 16 11:33:39 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sun Aug 16 11:34:13 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1736183b

sci-chemistry/autodock_vina: Require thread support in boost, bug #557822

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher  gentoo.org>

 sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 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 aea218f..a5662a1 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils flag-o-matic versionator
 
@@ -17,7 +17,7 @@ KEYWORDS="amd64 x86"
 LICENSE="Apache-2.0"
 IUSE="debug"
 
-RDEPEND="dev-libs/boost"
+RDEPEND="dev-libs/boost[threads]"
 DEPEND="${RDEPEND}"
 
 S="${WORKDIR}"/${MY_P}/build/linux/release