commit: 8c4e3b7978e2438bf5c9ae92fcb8422e88bc4a54 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Thu Jan 15 21:38:04 2026 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Fri Jan 16 11:55:56 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8c4e3b79
sci-chemistry/autodock_vina: add 1.2.7, EAPI-8, fixes build w/ boost-1.89 Closes: https://bugs.gentoo.org/963490 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-chemistry/autodock_vina/Manifest | 1 + .../autodock_vina/autodock_vina-1.2.7.ebuild | 46 ++++++++++++++++ .../files/autodock_vina-1.2.7-gentoo.patch | 64 ++++++++++++++++++++++ 3 files changed, 111 insertions(+) diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest index e4088c449178..2a6630f5033c 100644 --- a/sci-chemistry/autodock_vina/Manifest +++ b/sci-chemistry/autodock_vina/Manifest @@ -1,2 +1,3 @@ DIST autodock_vina-1.2.5.tar.gz 24158966 BLAKE2B c11493fcb35d409b97f639c4da48967d5df450781d412d80a951b95162555f4b1dfba809a01062136a7f0664c0b9a01a42b5403ee1d278a57afd669cf1f96321 SHA512 d36908e5833d22bcbc4dae353ef32b905d6eb46511302f7583a291398bfadff5e75fc99ce7b380860578b2257e5c32434cc75b1ca51fafb4b5f12d9477a878e9 +DIST autodock_vina-1.2.7.tar.gz 46488149 BLAKE2B 15ac50af12c6ac47b8ac6d8db6869a445b7535d72022934ec2658cbde2bb508fa36bfb932b2550fdef59342b98e2e604a4cf2a03a46e680781cefb47f2bb7b95 SHA512 b96d2f14bf26b63b3f132750e7b056632d8e48649ce24e267972e698d60b834c9dcd93907b22bd27413843a34112d6db32acef1793b8b2a5a14e813c66548633 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.7.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.2.7.ebuild new file mode 100644 index 000000000000..815c2ee186a7 --- /dev/null +++ b/sci-chemistry/autodock_vina/autodock_vina-1.2.7.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2026 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PN=AutoDock-Vina +inherit flag-o-matic toolchain-funcs + +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}"/${P}-gentoo.patch ) + +src_prepare() { + pushd "${WORKDIR}/${MY_PN}-${PV}" > /dev/null || die + sed -e "s:VERSION:\"${PV}\":g" \ + -i src/main/main.cpp \ + -i src/split/split.cpp || die + default + popd > /dev/null || die +} + +src_configure() { + append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -DBOOST_TIMER_ENABLE_DEPRECATED -std=c++14 +} + +src_compile() { + emake \ + BASE="${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-1.2.7-gentoo.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.7-gentoo.patch new file mode 100644 index 000000000000..86016aeb201d --- /dev/null +++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.7-gentoo.patch @@ -0,0 +1,64 @@ +diff -urN a/build/linux/debug/Makefile b/build/linux/debug/Makefile +--- a/build/linux/debug/Makefile ++++ b/build/linux/debug/Makefile +@@ -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 a/build/linux/release/Makefile b/build/linux/release/Makefile +--- a/build/linux/release/Makefile ++++ b/build/linux/release/Makefile +@@ -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 a/build/makefile_common b/build/makefile_common +--- a/build/makefile_common ++++ b/build/makefile_common +@@ -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_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 +
