commit: d9bb26b7ec22fed94308e440a16d54f4add8c956
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 15 21:39:35 2026 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Fri Jan 16 11:55:57 2026 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d9bb26b7
sci-chemistry/autodock_vina: drop 1.1.2-r1
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-chemistry/autodock_vina/Manifest | 1 -
.../autodock_vina/autodock_vina-1.1.2-r1.ebuild | 48 -------------
.../autodock_vina/files/1.1.2-gentoo.patch | 72 --------------------
.../autodock_vina-1.1.2-boost-filesystem.patch | 79 ----------------------
.../autodock_vina-1.1.2-missing-debug-decl.patch | 11 ---
5 files changed, 211 deletions(-)
diff --git a/sci-chemistry/autodock_vina/Manifest
b/sci-chemistry/autodock_vina/Manifest
index 2a6630f5033c..1416b5329553 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1,3 +1,2 @@
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-1.1.2-r1.ebuild
b/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
deleted file mode 100644
index 63810da09284..000000000000
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild
+++ /dev/null
@@ -1,48 +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_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/${MY_P}.tgz";
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="debug"
-
-RDEPEND="dev-libs/boost:="
-DEPEND="${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
- 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/1.1.2-gentoo.patch
b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
deleted file mode 100644
index 61ae8bec36f5..000000000000
--- a/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
+++ /dev/null
@@ -1,72 +0,0 @@
- build/linux/debug/Makefile | 2 +-
- build/linux/release/Makefile | 2 +-
- build/makefile_common | 14 +++++++-------
- 3 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile
-index 6a41cfc..8097fb9 100644
---- a/build/linux/debug/Makefile
-+++ b/build/linux/debug/Makefile
-@@ -1,7 +1,7 @@
- BASE=/usr/local
- BOOST_VERSION=1_41
- BOOST_INCLUDE = $(BASE)/include
--C_PLATFORM=-static -pthread
-+C_PLATFORM=-pthread
- GPP=/usr/local/bin/g++
- C_OPTIONS= -g
- BOOST_LIB_VERSION=
-diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile
-index 1de1063..ded8133 100644
---- a/build/linux/release/Makefile
-+++ b/build/linux/release/Makefile
-@@ -1,7 +1,7 @@
- BASE=/usr/local
- BOOST_VERSION=1_41
- BOOST_INCLUDE = $(BASE)/include
--C_PLATFORM=-static -pthread
-+C_PLATFORM=-pthread
- GPP=/usr/local/bin/g++
- C_OPTIONS= -O3 -DNDEBUG
- BOOST_LIB_VERSION=
-diff --git a/build/makefile_common b/build/makefile_common
-index a940329..96336e8 100644
---- a/build/makefile_common
-+++ b/build/makefile_common
-@@ -2,29 +2,29 @@ LIBOBJ = cache.o coords.o current_weights.o everything.o
grid.o szv_grid.o manif
- MAINOBJ = main.o
- SPLITOBJ = split.o
-
--INCFLAGS = -I $(BOOST_INCLUDE)
-+INCFLAGS = -I$(BOOST_INCLUDE)
-
- # -pedantic fails on Mac with Boost 1.41 (syntax problems in their headers)
- #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.
-
--LIBS = -l boost_system${BOOST_LIB_VERSION} -l
boost_thread${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 = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem
-lboost_program_options -lpthread
-
- .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/files/autodock_vina-1.1.2-boost-filesystem.patch
b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch
deleted file mode 100644
index 298aaa9ab993..000000000000
---
a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch
+++ /dev/null
@@ -1,79 +0,0 @@
- src/main/main.cpp | 10 +++++++++-
- src/split/split.cpp | 11 ++++++++++-
- 2 files changed, 19 insertions(+), 2 deletions(-)
-
-diff --git a/src/main/main.cpp b/src/main/main.cpp
-index f49c8f5..b566aa2 100644
---- a/src/main/main.cpp
-+++ b/src/main/main.cpp
-@@ -47,7 +47,7 @@
- using boost::filesystem::path;
-
- path make_path(const std::string& str) {
-- return path(str, boost::filesystem::native);
-+ return path(str);
- }
-
- void doing(int verbosity, const std::string& str, tee& log) {
-@@ -661,7 +661,11 @@ Thank you!\n";
- cpu, seed, verbosity, max_modes_sz,
energy_range, log);
- }
- catch(file_error& e) {
-+#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
-+ std::cerr << "\n\nError: could not open \"" << e.name.string()
<< "\" for " << (e.in ? "reading" : "writing") << ".\n";
-+#else
- std::cerr << "\n\nError: could not open \"" <<
e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") <<
".\n";
-+#endif
- return 1;
- }
- catch(boost::filesystem::filesystem_error& e) {
-@@ -673,7 +677,11 @@ Thank you!\n";
- return 1;
- }
- catch(parse_error& e) {
-+#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
-+ std::cerr << "\n\nParse error on line " << e.line << " in file
\"" << e.file.string() << "\": " << e.reason << '\n';
-+#else
- std::cerr << "\n\nParse error on line " << e.line << " in file
\"" << e.file.native_file_string() << "\": " << e.reason << '\n';
-+#endif
- return 1;
- }
- catch(std::bad_alloc&) {
-diff --git a/src/split/split.cpp b/src/split/split.cpp
-index 54c614b..bc5530e 100644
---- a/src/split/split.cpp
-+++ b/src/split/split.cpp
-@@ -38,7 +38,7 @@
- using boost::filesystem::path;
-
- path make_path(const std::string& str) {
-- return path(str, boost::filesystem::native);
-+ return path(str);
- }
-
- std::string default_prefix(const std::string& input_name, const std::string&
add) {
-@@ -208,7 +208,12 @@ Thank you!\n";
- write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);
- }
- catch(file_error& e) {
-+
-+#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
-+ std::cerr << "\n\nError: could not open \"" << e.name.string()
<< "\" for " << (e.in ? "reading" : "writing") << ".\n";
-+#else
- std::cerr << "\n\nError: could not open \"" <<
e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") <<
".\n";
-+#endif
- return 1;
- }
- catch(boost::filesystem::filesystem_error& e) {
-@@ -220,7 +225,11 @@ Thank you!\n";
- return 1;
- }
- catch(parse_error& e) {
-+#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
-+ std::cerr << "\n\nParse error on line " << e.line << " in file
\"" << e.file.string() << "\": " << e.reason << '\n';
-+#else
- std::cerr << "\n\nParse error on line " << e.line << " in file
\"" << e.file.native_file_string() << "\": " << e.reason << '\n';
-+#endif
- return 1;
- }
- catch(std::bad_alloc&) {
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
deleted file mode 100644
index c68adb1bff21..000000000000
---
a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-missing-debug-decl.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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))));
