gentoo auto-resync : 26:03:2024 - 13:01:14

5 files changed, 121 insertions, 1 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 2a59db27639d..0abb9286d626 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index ed2b6d0aa321..8cd80f22576c 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1,6 +1,9 @@
 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
+AUX autodock_vina-1.2.5-gentoo.patch 2803 BLAKE2B a365f3c83e5cfa366e458ce87e0d1e0a305b137040fbf3e0c0b2549e3cfde617c6934aaa4da6a992440400fbaa3f73b42faa665b1a5d1464f2a8d103b5469af3 SHA512 46b5c10123cf721eb80c6fa8d87f2d8405d269915d6bfec3eff5f1d5ee870e301608748ae245f7997f5c8a4b7c27e50fa222eff192c84ec4c82946c1783fa44b
+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
 EBUILD autodock_vina-1.1.2-r1.ebuild 972 BLAKE2B aaad2df1b51bdd684ca5fd9aaa54353b161e4e5d72b59210919349993fb6ad2c796f8b6bff4d420ad64e52273a26bf9f7d9b90f95387db5f7814352ebdb5be1c SHA512 123083cc13a05fd10627f9750274de9f7070e4068b718b4407230f9af22ead0a4f6ef33cda4b86a2d1e08856c31a58f8cc0d0ef8d861f196275332095885e44b
-MISC metadata.xml 911 BLAKE2B 67eb0088781bf4f791481c993f50fa034759baf858912b50a6bd650e275e95317c2460a69aa925d7c0955fd6e3fe70bda421f656c418a6f974686b148075a37f SHA512 0614ebad142dbebe4a9577a8c4fcbd2a5b18d5267b3be92531e6c118a21a9ef71addcf972eaa5710ba88daf0257c293d769ebd7153eda200ce530685bec76f85
+EBUILD autodock_vina-1.2.5.ebuild 1034 BLAKE2B a123bd340d3c5763d39cad3e2d9d7afbd6e4e0d96d1041736978af88295c58645e3ea53e634f1bb41e905d54afa94e8baa784fd27d6a6f577915e8c3635acdcc SHA512 383fa58b584f9f3ec6e1eb403b1845d3e7cfd66e88b89e857ffedc4847444caede2953f581f20b7414d5a9ec20e3f8bc4c864ded5206b182eb5c9ea38055401e
+MISC metadata.xml 1002 BLAKE2B 775eb10f8c916ff2b5655243224d1608a865228b1e300b636c793c1c86a4634a33fdda3bf4a8f56f43ad8bb734413963e490b738d2baf69168bb8dea6e3e6106 SHA512 0ea67a95d4bb8f90323ceeeced2d47f4732ee5fb3daa45d8690c13b71daf67729b33cdf3024a4706d2ee9e296b67474141125e95801b9f799228391571395532
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 000000000000..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 000000000000..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/Makefile	2024-03-05 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 ${BASE}/lib/libboost_thread${threadmt}${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_serialization${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_filesystem${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_program_options${BOOST_LIB_VERSION}.a
+ else
+-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${threadmt}${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
++LIBS = -l boost_system -l boost_thread -l boost_serialization -l boost_filesystem -l boost_program_options -l pthread
+ endif
+ 
+ .SUFFIXES: .cpp .o
+ 
+ %.o : ../../../src/lib/%.cpp 
+-	$(CC) $(CFLAGS) -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -o $@ -c $< 
+ 
+ %.o : ../../../src/design/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 	
+ %.o : ../../../src/main/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ %.o : ../../../src/split/%.cpp 
+-	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
++	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
+ 
+ all: vina vina_split
+ 
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
 	</longdescription>
+	<upstream>
+		<remote-id type="github">ccsb-scripps/AutoDock-Vina</remote-id>
+	</upstream>
 </pkgmetadata>