commit: e3a216cae029458db710a559f17121f08e7db69f Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Tue Jan 27 23:27:31 2026 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Wed Jan 28 18:30:48 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e3a216ca
sci-chemistry/autodock_vina: drop 1.2.5 Closes: https://bugs.gentoo.org/969024 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-chemistry/autodock_vina/Manifest | 1 - .../autodock_vina/autodock_vina-1.2.5.ebuild | 51 ----------------- .../files/autodock_vina-1.2.5-boost-1.85.patch | 21 ------- .../files/autodock_vina-1.2.5-gentoo.patch | 64 ---------------------- 4 files changed, 137 deletions(-) diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest index 1416b5329553..5fd6ce73bd36 100644 --- a/sci-chemistry/autodock_vina/Manifest +++ b/sci-chemistry/autodock_vina/Manifest @@ -1,2 +1 @@ -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 diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild deleted file mode 100644 index dd396732c357..000000000000 --- a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# 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}"/${P}-gentoo.patch - "${FILESDIR}"/${P}-boost-1.85.patch -) - -src_prepare() { - cd "${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-boost-1.85.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch deleted file mode 100644 index 55906b093a49..000000000000 --- a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch +++ /dev/null @@ -1,21 +0,0 @@ -https://bugs.gentoo.org/932237 ---- a/src/lib/vina.h -+++ b/src/lib/vina.h -@@ -35,7 +35,6 @@ - #include <boost/program_options.hpp> - #include <boost/filesystem/fstream.hpp> - #include <boost/filesystem/exception.hpp> --#include <boost/filesystem/convenience.hpp> // filesystem::basename - #include <boost/thread/thread.hpp> // hardware_concurrency // FIXME rm ? - #include <boost/algorithm/string.hpp> - //#include <openbabel/mol.h> ---- a/src/split/split.cpp -+++ b/src/split/split.cpp -@@ -30,7 +30,6 @@ - #include <boost/program_options.hpp> - #include <boost/filesystem/fstream.hpp> - #include <boost/filesystem/exception.hpp> --#include <boost/filesystem/convenience.hpp> // filesystem::basename - - #include "file.h" - #include "parse_error.h" 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 deleted file mode 100644 index e7bf1d5007ff..000000000000 --- a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch +++ /dev/null @@ -1,64 +0,0 @@ -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 -
