* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/, sci-chemistry/rosetta/files/
@ 2013-03-21 6:54 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2013-03-21 6:54 UTC (permalink / raw
To: gentoo-commits
commit: 70045b6378e4ed87c1a9414856a4e1dd28229eb2
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 19 15:16:35 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 19 15:16:35 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=70045b63
sci-chemistry/rosetta: Version Bump
Package-Manager: portage-2.2.0_alpha166
---
sci-chemistry/rosetta/ChangeLog | 15 +++-
.../rosetta/files/3.0-user-settings.patch | 26 ------
.../{3.0-boinc.patch => rosetta-3.4-boinc.patch} | 0
.../rosetta/files/rosetta-3.4-boost.patch | 16 ++++
....patch => rosetta-3.4-fix-scons-warnings.patch} | 0
...lgrind.patch => rosetta-3.4-fix-valgrind.patch} | 0
.../rosetta/files/rosetta-3.4-gcc4.7.patch | 32 +++++++
...0-platform.patch => rosetta-3.4-platform.patch} | 0
.../rosetta/files/rosetta-3.4-unbundle.patch | 47 ++++++++++
.../rosetta/files/rosetta-3.4-user-settings.patch | 29 ++++++
.../{3.0-zlib.patch => rosetta-3.4-zlib.patch} | 0
sci-chemistry/rosetta/metadata.xml | 26 +++---
.../{rosetta-3.0-r1.ebuild => rosetta-3.4.ebuild} | 96 +++++++++++---------
13 files changed, 203 insertions(+), 84 deletions(-)
diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog
index 62d5683..e13d7f3 100644
--- a/sci-chemistry/rosetta/ChangeLog
+++ b/sci-chemistry/rosetta/ChangeLog
@@ -1,7 +1,20 @@
# ChangeLog for sci-chemistry/rosetta
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*rosetta-3.4 (19 Mar 2013)
+
+ 19 Mar 2013; Justin Lecher <jlec@gentoo.org> -files/3.0-boinc.patch,
+ -rosetta-3.0-r1.ebuild, +rosetta-3.4.ebuild, +files/rosetta-3.4-boinc.patch,
+ -files/3.0-fix-scons-warnings.patch, +files/rosetta-3.4-boost.patch,
+ +files/rosetta-3.4-gcc4.7.patch, -files/3.0-fix-valgrind.patch,
+ +files/rosetta-3.4-fix-scons-warnings.patch,
+ +files/rosetta-3.4-platform.patch, -files/3.0-platform.patch,
+ +files/rosetta-3.4-fix-valgrind.patch, +files/rosetta-3.4-unbundle.patch,
+ -files/3.0-user-settings.patch, +files/rosetta-3.4-user-settings.patch,
+ -files/3.0-zlib.patch, +files/rosetta-3.4-zlib.patch, metadata.xml:
+ Version Bump
+
19 Sep 2010; Justin Lecher <jlec@gentoo.org> rosetta-3.0.ebuild,
rosetta-3.0-r1.ebuild:
virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl
diff --git a/sci-chemistry/rosetta/files/3.0-user-settings.patch b/sci-chemistry/rosetta/files/3.0-user-settings.patch
deleted file mode 100644
index bb1201b..0000000
--- a/sci-chemistry/rosetta/files/3.0-user-settings.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- tools/build/user.settings 2009-04-07 18:51:37.000000000 +0200
-+++ tools/build/user.settings.new 2009-04-07 18:51:37.000000000 +0200
-@@ -21,16 +21,22 @@
- settings = {
- "user" : {
- "prepends" : {
-+ "program_path" : os.environ["PATH"].split(":"),
-+ "include_path" : [ "/usr/include" ],
-+ "library_path" : [ "/usr/GENTOO_LIBDIR" ],
- },
- "appends" : {
- # Uncomment the line below and the "import os" line above
- # to let SCons find ICC (assuming it's on your PATH already)
-- "program_path" : os.environ["PATH"].split(":"),
-
- # Uncomment the line below to begin building the "devel" project too.
- #"projects": { "src" : [ "devel", ], },
- },
- "overrides" : {
-+ "flags" : {
-+ "compile" : [ GENTOO_CXXFLAGS ],
-+ "link" : [ GENTOO_LDFLAGS ],
-+ },
- },
- "removes" : {
- },
diff --git a/sci-chemistry/rosetta/files/3.0-boinc.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
similarity index 100%
rename from sci-chemistry/rosetta/files/3.0-boinc.patch
rename to sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
new file mode 100644
index 0000000..7c1e1ff
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
@@ -0,0 +1,16 @@
+ tools/build/basic.settings | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tools/build/basic.settings b/tools/build/basic.settings
+index ecf3237..356cd61 100644
+--- a/tools/build/basic.settings
++++ b/tools/build/basic.settings
+@@ -610,7 +610,7 @@ settings = {
+ "gcc, boost_thread" : {
+ "appends" : {
+ "defines" : [ "MULTI_THREADED" ],
+- "libraries" : [ "pthread", "boost_thread" ],
++ "libraries" : [ "pthread", "boost_thread", "boost_system" ],
+ "library_path" : [ "/usr/local/lib", "/opt/boost/lib" ],
+ "flags" : {
+ "compile" : [ "pthread" ],
diff --git a/sci-chemistry/rosetta/files/3.0-fix-scons-warnings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
similarity index 100%
rename from sci-chemistry/rosetta/files/3.0-fix-scons-warnings.patch
rename to sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
diff --git a/sci-chemistry/rosetta/files/3.0-fix-valgrind.patch b/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
similarity index 100%
rename from sci-chemistry/rosetta/files/3.0-fix-valgrind.patch
rename to sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
new file mode 100644
index 0000000..d0893c1
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
@@ -0,0 +1,32 @@
+ tools/build/options.settings | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tools/build/options.settings b/tools/build/options.settings
+index 30fb65e..f79ef5b 100644
+--- a/tools/build/options.settings
++++ b/tools/build/options.settings
+@@ -9,7 +9,7 @@
+ options = {
+
+ "cxx" : {
+- "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
++ "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "*" ],
+ "icc" : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
+ "msvc" : [ "7.0", "7.1", "8.0", "8.1", "*" ],
+ "xlc" : [ "7.0", "8.0", "9.0", "XL", "*" ],
+ src/protocols/jd2/SingleFileBuffer.cc | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
+index aa78d91..61ca823 100644
+--- a/src/protocols/jd2/SingleFileBuffer.cc
++++ b/src/protocols/jd2/SingleFileBuffer.cc
+@@ -28,6 +28,8 @@
+ #include <ctime> // for clock()
+ #endif
+
++#include <unistd.h>
++
+ namespace protocols {
+ namespace jd2 {
+ using namespace core;
diff --git a/sci-chemistry/rosetta/files/3.0-platform.patch b/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
similarity index 100%
rename from sci-chemistry/rosetta/files/3.0-platform.patch
rename to sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
new file mode 100644
index 0000000..ba810b1
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
@@ -0,0 +1,47 @@
+ src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh | 3 +--
+ .../pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh | 3 +--
+ src/utility/io/zipstream.hpp | 3 +--
+ 3 files changed, 3 insertions(+), 6 deletions(-)
+
+diff --git a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
+index 0aa44a6..299e0c5 100644
+--- a/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
++++ b/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
+@@ -402,8 +402,7 @@
+ #include <boost/function.hpp>
+ #include <boost/pool/detail/mutex.hpp>
+ #include <boost/pool/poolfwd.hpp>
+-#include <zlib/zlib.h>
+-#include <zlib/zutil.h>
++#include <zlib.h>
+
+ namespace core {
+ namespace pack {
+diff --git a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
+index 2396126..700e78d 100644
+--- a/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
++++ b/src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
+@@ -405,8 +405,7 @@
+ #include <boost/function.hpp>
+ #include <boost/pool/detail/mutex.hpp>
+ #include <boost/pool/poolfwd.hpp>
+-#include <zlib/zlib.h>
+-#include <zlib/zutil.h>
++#include <zlib.h>
+
+ namespace core {
+ namespace pack {
+diff --git a/src/utility/io/zipstream.hpp b/src/utility/io/zipstream.hpp
+index adaf88c..c7d36d0 100644
+--- a/src/utility/io/zipstream.hpp
++++ b/src/utility/io/zipstream.hpp
+@@ -43,8 +43,7 @@
+
+
+ // Zlib headers
+-#include <zlib/zlib.h>
+-#include <zlib/zutil.h>
++#include <zlib.h>
+
+
+
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch b/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
new file mode 100644
index 0000000..d7297cf
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
@@ -0,0 +1,29 @@
+ tools/build/user.settings | 8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
+
+diff --git a/tools/build/user.settings b/tools/build/user.settings
+index 27a001f..9696e3e 100644
+--- a/tools/build/user.settings
++++ b/tools/build/user.settings
+@@ -22,7 +22,7 @@
+ # and select between them from the options. For now there is only the
+ # single "user" settings.
+
+-#import os
++import os
+ settings = {
+ "user" : {
+ "prepends" : {
+@@ -38,6 +38,12 @@ settings = {
+ #"program_path" : os.environ["PATH"].split(":"),
+ },
+ "overrides" : {
++ "flags" : {
++ "compile" : [ GENTOO_CXXFLAGS ],
++ "link" : [ GENTOO_LDFLAGS ],
++ },
++ "cc" : os.environ["CC"],
++ "cxx" : os.environ["CXX"],
+ },
+ "removes" : {
+ },
diff --git a/sci-chemistry/rosetta/files/3.0-zlib.patch b/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
similarity index 100%
rename from sci-chemistry/rosetta/files/3.0-zlib.patch
rename to sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml
index 6db8765..3468184 100644
--- a/sci-chemistry/rosetta/metadata.xml
+++ b/sci-chemistry/rosetta/metadata.xml
@@ -1,17 +1,17 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
-<use>
- <flag name='boinc'>compile rosetta as a rosetta@home client</flag>
- <flag name='boost'>compile rosetta with boost supported code</flag>
-</use>
-<upstream>
- <bugs-to>general-support@mail.rosettacommons.org</bugs-to>
-</upstream>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>sci@gentoo.org</email>
+ </maintainer>
+ <use>
+ <flag name="boinc">compile rosetta as a rosetta@home client</flag>
+ <flag name="boost">compile rosetta with boost supported code</flag>
+ <flag name="float">Build with floats rather than doubles</flag>
+ <flag name="custom-flags">Use your own flags</flag>
+ </use>
+ <upstream>
+ <bugs-to>general-support@mail.rosettacommons.org</bugs-to>
+ </upstream>
</pkgmetadata>
-
-
diff --git a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
similarity index 55%
rename from sci-chemistry/rosetta/rosetta-3.0-r1.ebuild
rename to sci-chemistry/rosetta/rosetta-3.4.ebuild
index da1d226..e38bbcf 100644
--- a/sci-chemistry/rosetta/rosetta-3.0-r1.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -1,14 +1,15 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
# boinc support is BROKEN !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-EAPI="2"
+EAPI=5
-inherit eutils multilib versionator
+inherit eutils multilib prefix scons-utils toolchain-funcs versionator
-MY_P="${PN}$(get_major_version)_source"
+#MY_P="${PN}$(get_major_version)_source"
+MY_P="${PN}${PV}_source"
DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions"
HOMEPAGE="http://www.rosettacommons.org/"
@@ -16,43 +17,53 @@ SRC_URI="${MY_P}.tgz"
LICENSE="|| ( rosetta-academic rosetta-commercial )"
SLOT="0"
-KEYWORDS=""
-IUSE="boinc boost debug doc mpi X"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="boinc +boost custom-flags debug doc float mpi +openmp X"
+
+REQUIRED_USE="?? ( mpi boinc )"
+
RESTRICT="fetch"
-RDEPEND="mpi? ( virtual/mpi )
+RDEPEND="
+ dev-db/cppdb
+ mpi? ( virtual/mpi )
boinc? ( sci-misc/boinc[X?] )
boost? ( dev-libs/boost )
sci-libs/rosetta-db"
DEPEND="${RDEPEND}
- >=dev-util/scons-0.96.1
+ dev-util/scons
doc? ( app-doc/doxygen )
X? ( media-libs/freeglut )"
MYCONF=""
-S="${WORKDIR}/${MY_P}"
+S="${WORKDIR}/${PN}_source"
pkg_nofetch() {
einfo "Go to ${HOMEPAGE} and get ${A}"
einfo "which must be placed in ${DISTDIR}"
}
-pkg_setup() {
- use mpi && use boinc && \
- die "you can either use mpi or boinc support"
-}
-
src_prepare() {
local myCXXFLAGS
local myLDFLAGS
- epatch "${FILESDIR}"/${PV}-platform.patch
- epatch "${FILESDIR}"/${PV}-fix-scons-warnings.patch
- epatch "${FILESDIR}"/${PV}-user-settings.patch
- epatch "${FILESDIR}"/${PV}-fix-valgrind.patch
- epatch "${FILESDIR}"/${PV}-boinc.patch
- rm bin/* -fv
+ use custom-flags || \
+ export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
+
+ epatch \
+ "${FILESDIR}"/${P}-platform.patch \
+ "${FILESDIR}"/${P}-user-settings.patch \
+ "${FILESDIR}"/${P}-fix-valgrind.patch \
+ "${FILESDIR}"/${P}-boinc.patch \
+ "${FILESDIR}"/${P}-boost.patch \
+ "${FILESDIR}"/${P}-gcc4.7.patch
+
+ eprefixify tools/build/*
+
+ rm bin/* external/{dbio,scons-local,lib} -rfv || die
+
+ find external/boost_1_46_1 -name "*.hpp" -delete || die
for i in ${CXXFLAGS}; do
myCXXFLAGS="${myCXXFLAGS} \"${i/-/}\","
@@ -62,14 +73,19 @@ src_prepare() {
myLDFLAGS="${myLDFLAGS} \"${i/-/}\","
done
- sed -e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
+ sed \
+ -e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
-e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \
-e "s:GENTOO_LIBDIR:$(get_libdir):g" \
- -i tools/build/user.settings
+ -i tools/build/user.settings || die
- use mpi && \
- sed -e 's:mpiCC:mpicxx:g' \
- -i tools/build/basic.settings
+ if use mpi; then
+ sed \
+ -e 's:mpiCC:mpicxx:g' \
+ -i tools/build/basic.settings || die
+ fi
+
+ tc-export CC CXX
}
src_configure() {
@@ -77,8 +93,11 @@ src_configure() {
local mymode=""
local mycxx=""
- use boinc && EXTRAS="boinc"
+ use boinc && EXTRAS="boinc"
use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost")
+ use boost && EXTRAS=$(my_list_append "${EXTRAS}" "boost_thread")
+ use float && EXTRAS=$(my_list_append "${EXTRAS}" "rosetta_float")
+ use openmp && EXTRAS=$(my_list_append "${EXTRAS}" "omp")
use X && EXTRAS=$(my_list_append "${EXTRAS}" "graphics")
use mpi && EXTRAS=$(my_list_append "${EXTRAS}" "mpi")
@@ -93,15 +112,12 @@ src_configure() {
mymode="release"
fi
- MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "--load-average[=0-9.]*")
- MAKEOPTS=$(my_filter_option "${MAKEOPTS}" "-l[0-9.]*")
-
- MYCONF="${MAKEOPTS} mode=${mymode} ${myextras} ${mycxx}"
+ MYCONF="mode=${mymode} ${myextras} ${mycxx}"
}
src_compile() {
einfo "running 'scons bin cat=src ${MYCONF}' ..."
- scons bin cat=src ${MYCONF} || die "scons bin cat=src ${MYCONF} failed"
+ escons bin cat=src ${MYCONF}
if use doc; then
einfo "running 'scons ${MYCONF} cat=doc' ..."
@@ -110,25 +126,17 @@ src_compile() {
}
src_install() {
- local BIT
-
- use amd64 && BIT="64"
- use x86 && BIT="32"
+ dolib.so build/src/release/linux/*/*/*/*/*/${EXTRAS//,/-}/*.so*
- dolib.so build/src/release/linux/2.6/${BIT}/x86/${COMPILER}/${EXTRAS//,/-}/*.so || \
- die "failed to install libs"
-
- if use doc; then
- dohtml build/doc/rosetta++/docs/* || die "could not install docs"
- fi
+ use doc && dohtml build/doc/rosetta++/docs/*
- cd bin
+ cd bin || die
for BIN in *; do
newbin ${BIN} ${BIN%%.*} || die "could not install rosetta program files"
done
- mv "${D}"/usr/bin/cluster{,-${PN}}
- mv "${D}"/usr/bin/benchmark{,-${PN}}
+ mv "${ED}"/usr/bin/cluster{,-${PN}} || die
+ mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
}
my_filter_option() {
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/, sci-chemistry/rosetta/files/
@ 2013-06-11 14:25 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2013-06-11 14:25 UTC (permalink / raw
To: gentoo-commits
commit: cfad9afcc75652e395adf780dfb3a2d4df72a032
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 11 12:12:17 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 14:22:52 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cfad9afc
update to new lange patches
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
.../rosetta/files/rosetta-3.4-gcc4.78.patch | 32 ++++++++++++++++++++++
.../rosetta/files/rosetta-3.4-lange-fix.patch | 22 +++++++++++++++
sci-chemistry/rosetta/rosetta-3.4.ebuild | 12 ++++++--
3 files changed, 63 insertions(+), 3 deletions(-)
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
new file mode 100644
index 0000000..882534b
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
@@ -0,0 +1,32 @@
+ tools/build/options.settings | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tools/build/options.settings b/tools/build/options.settings
+index 30fb65e..f79ef5b 100644
+--- a/tools/build/options.settings
++++ b/tools/build/options.settings
+@@ -9,7 +9,7 @@
+ options = {
+
+ "cxx" : {
+- "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
++ "gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "*" ],
+ "icc" : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
+ "msvc" : [ "7.0", "7.1", "8.0", "8.1", "*" ],
+ "xlc" : [ "7.0", "8.0", "9.0", "XL", "*" ],
+ src/protocols/jd2/SingleFileBuffer.cc | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
+index aa78d91..61ca823 100644
+--- a/src/protocols/jd2/SingleFileBuffer.cc
++++ b/src/protocols/jd2/SingleFileBuffer.cc
+@@ -28,6 +28,8 @@
+ #include <ctime> // for clock()
+ #endif
+
++#include <unistd.h>
++
+ namespace protocols {
+ namespace jd2 {
+ using namespace core;
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
new file mode 100644
index 0000000..17e85f8
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
@@ -0,0 +1,22 @@
+ tools/build/setup.py | 8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
+
+diff --git a/tools/build/setup.py b/tools/build/setup.py
+index 4e57ff6..d8a2a08 100644
+--- a/tools/build/setup.py
++++ b/tools/build/setup.py
+@@ -354,7 +354,13 @@ what SCons will use to build the system.
+ symbols = setting.appends.symbols()
+ if symbols.has_key("ENV"):
+ for key, value in symbols["ENV"].items():
+- env["ENV"][key] += value
++ if key == "PATH":
++ env["ENV"][key] = value
++ else:
++ try:
++ env["ENV"][key] += value
++ except:
++ print key, value
+ del symbols["ENV"]
+ env.Append(**symbols)
+ if setting.prepends:
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index 6ffe8df..518e746 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -13,12 +13,12 @@ MY_P="${PN}${PV}_source"
DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions"
HOMEPAGE="http://www.rosettacommons.org/"
-SRC_URI="${MY_P}.tgz"
+SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt"
LICENSE="|| ( rosetta-academic rosetta-commercial )"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boinc +boost custom-cflags debug doc float mpi +openmp X"
+IUSE="boinc +boost custom-cflags debug doc float +lange mpi +openmp X"
REQUIRED_USE="?? ( mpi boinc )"
@@ -51,13 +51,19 @@ src_prepare() {
use custom-cflags || \
export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
+ export LD_LIBRARY_PATH=""
+ use lange && \
+ epatch \
+ "${DISTDIR}"/patch_${PN}${PV}_to_CSROSETTA3_ver1.3.txt \
+ "${FILESDIR}"/${P}-lange-fix.patch
+
epatch \
"${FILESDIR}"/${P}-platform.patch \
"${FILESDIR}"/${P}-user-settings.patch \
"${FILESDIR}"/${P}-fix-valgrind.patch \
"${FILESDIR}"/${P}-boinc.patch \
"${FILESDIR}"/${P}-boost.patch \
- "${FILESDIR}"/${P}-gcc4.7.patch
+ "${FILESDIR}"/${P}-gcc4.78.patch
eprefixify tools/build/*
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2013-06-11 14:25 [gentoo-commits] proj/sci:master commit in: sci-chemistry/rosetta/, sci-chemistry/rosetta/files/ Justin Lecher
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2013-03-21 6:54 Justin Lecher
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