proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

6 files changed, 296 insertions, 0 deletions

diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
new file mode 100644
index 000000000000..a2f7882e9d79
--- /dev/null
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -0,0 +1 @@
+DIST autodock_vina_1_1_2.tgz 67366 SHA256 b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776 SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 WHIRLPOOL b68f3bb81fe957fddb6674f71e0c63d1425eb5b4de0615258545ba8e241b347380c8745ee47bd2ee2257f29916191773440e3dd4e9ce857b83a947074eae8d45
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
new file mode 100644
index 000000000000..aea218f8faf9
--- /dev/null
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils flag-o-matic versionator
+
+MY_P="${PN}_$(replace_all_version_separators _)"
+
+DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
+HOMEPAGE="http://vina.scripps.edu/"
+SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+LICENSE="Apache-2.0"
+IUSE="debug"
+
+RDEPEND="dev-libs/boost"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_P}/build/linux/release
+
+src_prepare() {
+	cd "${WORKDIR}"/${MY_P} || die
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/${P}-boost-filesystem.patch
+}
+
+src_compile() {
+	local c_options
+
+	use debug || c_options="-DNDEBUG"
+
+	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3
+
+	emake \
+		BASE="${EPREFIX}"/usr/ \
+		GPP="$(tc-getCXX)" \
+		C_OPTIONS="${c_options}"
+}
+
+src_install() {
+	dobin vina{,_split}
+}
diff --git a/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch
new file mode 100644
index 000000000000..356ae2ee547d
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/1.1.1-gentoo.patch
@@ -0,0 +1,68 @@
+diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile
+index d2c2d3b..d1f02e5 100644
+--- a/build/linux/debug/Makefile
++++ b/build/linux/debug/Makefile
+@@ -1,6 +1,6 @@
+ BASE=/usr/local
+ BOOST_VERSION=1_41
+-C_PLATFORM=-static-libgcc -pthread
++C_PLATFORM=-pthread
+ GPP=/usr/bin/g++
+ C_OPTIONS= -g
+ BOOST_LIB_VERSION=
+diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile
+index bfbcc1e..c9fd630 100644
+--- a/build/linux/release/Makefile
++++ b/build/linux/release/Makefile
+@@ -1,6 +1,6 @@
+ BASE=/usr/local
+ BOOST_VERSION=1_41
+-C_PLATFORM=-static-libgcc -pthread
++C_PLATFORM=-pthread
+ GPP=/usr/bin/g++
+ C_OPTIONS= -O3 -DNDEBUG
+ BOOST_LIB_VERSION=
+diff --git a/build/makefile_common b/build/makefile_common
+index 885935c..e72142d 100644
+--- a/build/makefile_common
++++ b/build/makefile_common
+@@ -1,30 +1,30 @@
+-BOOST_INCLUDE = $(BASE)/include/boost-${BOOST_VERSION}
++BOOST_INCLUDE = $(BASE)/include/boost
+ 
+ LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o
+ MAINOBJ = main.o
+ SPLITOBJ = split.o
+ 
+-INCFLAGS = -I $(BOOST_INCLUDE)
++INCFLAGS = -I$(BOOST_INCLUDE)
+ 
+-CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
++CC = ${GPP} ${C_PLATFORM} ${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/1.1.2-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
new file mode 100644
index 000000000000..61ae8bec36f5
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch
@@ -0,0 +1,72 @@
+ 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
new file mode 100644
index 000000000000..298aaa9ab993
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch
@@ -0,0 +1,79 @@
+ 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/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml
new file mode 100644
index 000000000000..3f44e973345a
--- /dev/null
+++ b/sci-chemistry/autodock_vina/metadata.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+  <longdescription>
+AutoDock Vina is a new open-source program for drug discovery, molecular
+docking and virtual screening, offering multi-core capability, high
+performance and enhanced accuracy and ease of use. [1]
+AutoDock Vina has been designed and implemented by Dr. Oleg Trott
+in the Molecular Graphics Lab at The Scripps Research Institute.
+If you used AutoDock Vina in your work, please cite:
+O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy
+of docking with a new scoring function, efficient optimization and
+multithreading
+Journal of Computational Chemistry 31 (2010) 455-461
+</longdescription>
+  <!--
+<use>
+  <flag name='flag'>Description of how USE='flag' affects this package</flag>
+  <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this
+	  package</flag>
+  <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking.
+	  Requires an installed dictionary from <cat>app-dicts</cat></flag>
+</use>
+-->
+</pkgmetadata>