commit: 1c4cc4b44ec299a0611ea194f3ffc4c8b6389f87
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 08:34:14 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 08:43:32 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c4cc4b4
sci-chemistry/rosetta: removed unmaintained package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../rosetta/files/rosetta-3.4-boinc.patch | 53 -------
.../rosetta/files/rosetta-3.4-boost.patch | 16 --
.../rosetta/files/rosetta-3.4-boost157.patch | 16 --
.../files/rosetta-3.4-fix-scons-warnings.patch | 82 ----------
.../rosetta/files/rosetta-3.4-fix-valgrind.patch | 11 --
.../rosetta/files/rosetta-3.4-gcc4.7.patch | 32 ----
.../rosetta/files/rosetta-3.4-gcc4.78.patch | 32 ----
.../rosetta/files/rosetta-3.4-gcc4.789.patch | 32 ----
.../rosetta/files/rosetta-3.4-lange-fix.patch | 22 ---
.../rosetta/files/rosetta-3.4-platform.patch | 11 --
.../rosetta/files/rosetta-3.4-unbundle.patch | 47 ------
.../rosetta/files/rosetta-3.4-user-settings.patch | 29 ----
sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch | 12 --
sci-chemistry/rosetta/metadata.xml | 17 --
sci-chemistry/rosetta/rosetta-3.4.ebuild | 171 ---------------------
15 files changed, 583 deletions(-)
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
deleted file mode 100644
index 1f6da965c..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boinc.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- src/protocols/boinc/boinc_shmem.hh 2009-02-03 22:47:07.000000000 +0100
-+++ src/protocols/boinc/boinc_shmem.hh.new 2009-04-09 14:59:15.000000000
+0200
-@@ -18,7 +18,7 @@
- #include <core/types.hh>
-
- #ifdef BOINC
--#include "boinc_api.h"
-+#include "boinc/boinc_api.h"
- #endif
-
- namespace protocols {
---- src/protocols/boinc/boinc.hh 2009-02-03 22:47:07.000000000 +0100
-+++ src/protocols/boinc/boinc.hh.new 2009-04-09 15:00:57.000000000 +0200
-@@ -20,11 +20,11 @@
- #include <boinc_win.h>
- #include <str_util.h>
- #endif
--#include <boinc_api.h>
--#include <diagnostics.h>
--#include <error_numbers.h>
-+#include <boinc/boinc_api.h>
-+#include <boinc/diagnostics.h>
-+#include <boinc/error_numbers.h>
- #ifdef BOINC_GRAPHICS
--#include <graphics2.h>
--#include <util.h>
--#include <shmem.h>
-+#include <boinc/graphics2.h>
-+#include <boinc/util.h>
-+#include <boinc/shmem.h>
-
---- src/utility/exit.cc 2009-02-03 22:47:28.000000000 +0100
-+++ src/utility/exit.cc.new 2009-04-09 16:23:18.000000000 +0200
-@@ -23,7 +23,7 @@
- // Boinc headers
- #ifdef BOINC
- #include <utility/io/izstream.hh>
--#include <boinc_api.h>
-+#include <boinc/boinc_api.h>
- #include <string>
- #endif
-
---- src/utility/boinc/boinc_util.cc 2009-02-03 22:47:30.000000000 +0100
-+++ src/utility/boinc/boinc_util.cc.new 2009-04-09 16:25:16.000000000
+0200
-@@ -20,7 +20,7 @@
- //#ifdef _WIN32
- //#include <boinc_win.h>
- //#endif
--#include <boinc_api.h>
-+#include <boinc/boinc_api.h>
-
- // C++ headers
- #include <iostream>
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
deleted file mode 100644
index 7c1e1ffc2..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- 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/rosetta-3.4-boost157.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch
deleted file mode 100644
index c2d7594b6..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/protocols/moves/StructureRestrictor.cc | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/protocols/moves/StructureRestrictor.cc
b/src/protocols/moves/StructureRestrictor.cc
-index 1e1f1d4..da69796 100644
---- a/src/protocols/moves/StructureRestrictor.cc
-+++ b/src/protocols/moves/StructureRestrictor.cc
-@@ -40,7 +40,7 @@
-
- using namespace std;
- using namespace boost;
--using namespace core;
-+using namespace boost::core;
- using namespace pose;
- using namespace protocols::jd2;
-
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
deleted file mode 100644
index 321d0a784..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-scons-warnings.patch
+++ /dev/null
@@ -1,82 +0,0 @@
---- src/SConscript.src 2009-02-03 22:44:31.000000000 +0100
-+++ src/SConscript.src.new 2009-04-07 16:25:30.000000000 +0200
-@@ -85,7 +85,7 @@
-
- # Transform the modified settings into SCons Environment variables.
- # Gives priority to project settings over global settings.
--env = build.environment.Copy()
-+env = build.environment.Clone()
- env.Prepend(**actual.symbols())
-
-
---- tools/build/setup.py 2009-02-03 22:44:32.000000000 +0100
-+++ tools/build/setup.py.new 2009-04-07 16:43:42.000000000 +0200
-@@ -42,21 +42,21 @@
- # Read in the options from the .settings files (1st pass)
- # This has to be done in two passes, because some legal values
- # (version numbers) are dependent on the other values
-- options.AddOptions(
-+ options.AddVariables(
- # Options for the build. Modifiable on the command-line.
-- EnumOption("cxx", "Select the C++ compiler to build with",
-+ EnumVariable("cxx", "Select the C++ compiler to build with",
- defaults.cxx, supported.cxx),
-- EnumOption("os", "Select the operating system to build for",
-+ EnumVariable("os", "Select the operating system to build for",
- defaults.os, supported.os),
-- EnumOption("arch", "Select the processor architecture to build for",
-+ EnumVariable("arch", "Select the processor architecture to build for",
- defaults.arch, supported.arch),
-- EnumOption("mode", "Select the optimization mode",
-+ EnumVariable("mode", "Select the optimization mode",
- defaults.mode, supported.mode),
-- ListOption("cat", "Select the build category",
-+ ListVariable("cat", "Select the build category",
- defaults.cat, supported.cat),
-- ListOption("extras", "Select any extras",
-+ ListVariable("extras", "Select any extras",
- defaults.extras, supported.extras),
-- ListOption("log", "Log debugging output",
-+ ListVariable("log", "Log debugging output",
- defaults.log, supported.log),
- )
-
---- tools/build/setup.py 2009-04-07 16:44:26.000000000 +0200
-+++ tools/build/setup.py.new 2009-04-07 16:46:45.000000000 +0200
-@@ -37,7 +37,7 @@
-
- # Incorporate options in site and user options
- option_files = [ "%s.options" % (name) for name in ("site", "user") ]
-- options = Options(option_files)
-+ options = Variables(option_files)
-
- # Read in the options from the .settings files (1st pass)
- # This has to be done in two passes, because some legal values
-@@ -68,12 +68,12 @@
- cxx = env["cxx"]
- os = env["os"]
- arch = env["arch"]
-- options.AddOptions(
-- EnumOption("cxx_ver", "Select the C++ compiler version",
-+ options.AddVariables(
-+ EnumVariable("cxx_ver", "Select the C++ compiler version",
- defaults.cxx_ver, supported.cxx[cxx]),
-- EnumOption("os_ver", "Select the operating system version",
-+ EnumVariable("os_ver", "Select the operating system version",
- defaults.os_ver, supported.os[os]),
-- EnumOption("arch_size", "Select the architecture bit-size",
-+ EnumVariable("arch_size", "Select the architecture bit-size",
- defaults.arch_size, supported.arch[arch]),
- )
-
---- src/SConscript.apps 2009-02-03 22:44:31.000000000 +0100
-+++ src/SConscript.apps.new 2009-04-07 16:48:06.000000000 +0200
-@@ -92,7 +92,7 @@
-
- # Transform the modified settings into SCons Environment variables.
- # Gives priority to project settings over global settings.
--env = build.environment.Copy()
-+env = build.environment.Clone()
- env.Prepend(**actual.symbols())
- if "static" not in build.options.extras:
- env["RPATH"] = build.toplevel + "/build/src/" + build.platform
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
deleted file mode 100644
index bc98773c1..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-fix-valgrind.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- tools/build/options.settings 2009-02-03 22:44:32.000000000 +0100
-+++ tools/build/options.settings.new 2009-04-07 18:12:00.000000000 +0200
-@@ -76,7 +76,7 @@
- # Build so that valgrind can follow the memory use.
- # Valgrind normally works fine with most executables but not
- # with static builds, which we are doing.
-- "valgrind",
-+ "shared",
-
- # Build using static linking.
- "static",
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
deleted file mode 100644
index d0893c183..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.7.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- 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/rosetta-3.4-gcc4.78.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
deleted file mode 100644
index 882534bfd..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- 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-gcc4.789.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch
deleted file mode 100644
index e11532ac4..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- 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", "4.9", "*" ],
- "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
deleted file mode 100644
index 17e85f882..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
+++ /dev/null
@@ -1,22 +0,0 @@
- 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/files/rosetta-3.4-platform.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
deleted file mode 100644
index 82f0ba63f..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-platform.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./tools/build/setup_platforms.py 2009-02-03 22:44:32.000000000 +0100
-+++ ./tools/build/setup_platforms.py.new 2009-04-07 16:16:44.000000000
+0200
-@@ -274,7 +274,7 @@
- """
- # Note that these are very different values, and need processing
- if globals().has_key("platform"):
-- return platform.processor() or _uname()[4]
-+ return platform.machine() or _uname()[4]
- else:
- return _uname()[4]
-
diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
deleted file mode 100644
index ba810b162..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-unbundle.patch
+++ /dev/null
@@ -1,47 +0,0 @@
- 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
deleted file mode 100644
index d7297cfc0..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-user-settings.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- 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/rosetta-3.4-zlib.patch
b/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
deleted file mode 100644
index 18060add4..000000000
--- a/sci-chemistry/rosetta/files/rosetta-3.4-zlib.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/utility/io/zipstream.hpp 2009-02-03 22:47:27.000000000 +0100
-+++ src/utility/io/zipstream.hpp.new 2009-04-07 19:57:09.000000000 +0200
-@@ -36,8 +36,7 @@
-
-
- // Zlib headers
--#include <zlib/zlib.h>
--#include <zlib/zutil.h>
-+#include <zlib.h>
-
- // C++ headers
- #include <algorithm>
diff --git a/sci-chemistry/rosetta/metadata.xml
b/sci-chemistry/rosetta/metadata.xml
deleted file mode 100644
index dcf5c02f4..000000000
--- a/sci-chemistry/rosetta/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Chemistry Project</name>
- </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="lange">Apply patches from www.csrosetta.org</flag>
- </use>
- <upstream>
-
<bugs-to>mailto:[email protected]</bugs-to>
- </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild
b/sci-chemistry/rosetta/rosetta-3.4.ebuild
deleted file mode 100644
index bf40276a7..000000000
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ /dev/null
@@ -1,171 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-# boinc support is BROKEN !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EAPI=5
-
-inherit eutils multilib prefix scons-utils toolchain-funcs versionator
-
-#MY_P="${PN}$(get_major_version)_source"
-MY_P="${PN}${PV}_source"
-
-DESCRIPTION="Prediction of protein structures and protein-protein interactions"
-HOMEPAGE="http://www.rosettacommons.org/";
-SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt"
-
-LICENSE="|| ( rosetta-academic rosetta-commercial )"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boinc +boost custom-cflags debug doc float +lange mpi +openmp X"
-
-REQUIRED_USE="?? ( mpi boinc )"
-
-RESTRICT="fetch"
-
-RDEPEND="
- dev-db/cppdb
- mpi? ( virtual/mpi )
- boinc? ( sci-misc/boinc[X?] )
- boost? ( dev-libs/boost )
- sci-libs/rosetta-db"
-DEPEND="${RDEPEND}
- dev-util/scons
- doc? ( app-doc/doxygen )
- X? ( media-libs/freeglut )"
-
-MYCONF=""
-
-S="${WORKDIR}/${PN}_source"
-
-pkg_nofetch() {
- einfo "Go to ${HOMEPAGE} and get ${A}"
- einfo "which must be placed in ${DISTDIR}"
-}
-
-src_prepare() {
- local myCXXFLAGS
- local myLDFLAGS
-
- use custom-cflags || \
- export CXXFLAGS="-O3 -ffast-math -funroll-loops
-finline-functions -finline-limit=20000 -pipe"
-
- export LD_LIBRARY_PATH=""
- use lange && \
- epatch \
- "${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}-boost157.patch \
- "${FILESDIR}"/${P}-gcc4.789.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/-/}\","
- done
-
- for i in ${LDFLAGS}; do
- myLDFLAGS="${myLDFLAGS} \"${i/-/}\","
- done
-
- sed \
- -e "s:GENTOO_CXXFLAGS:${myCXXFLAGS}:g" \
- -e "s:GENTOO_LDFLAGS:${myCXXFLAGS} ${myLDFLAGS}:g" \
- -e "s:GENTOO_LIBDIR:$(get_libdir):g" \
- -e "/program_path/s:#::g" \
- -i tools/build/user.settings || die
-
- tc-export CC CXX
-
- if use mpi; then
- sed \
- -e 's:mpiCC:mpicxx:g' \
- -i tools/build/basic.settings || die
- sed \
- -e "/cxx/d" \
- -i tools/build/user.settings || die
- fi
-}
-
-src_configure() {
- local myextras=""
- local mymode=""
- local mycxx=""
-
- 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")
-
- COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
- mycxx="cxx=${COMPILER}"
-
- test -n "${EXTRAS}" && myextras="extras=${EXTRAS}"
-
- if use debug; then
- mymode="debug"
- else
- mymode="release"
- fi
-
- MYCONF="mode=${mymode} ${myextras} ${mycxx}"
-}
-
-src_compile() {
- einfo "running 'scons bin cat=src ${MYCONF}' ..."
- escons bin cat=src ${MYCONF}
-
- if use doc; then
- einfo "running 'scons ${MYCONF} cat=doc' ..."
- scons ${MYCONF} cat=doc || die "scons failed to build
documentation"
- fi
-}
-
-src_install() {
- dolib.so build/src/release/linux/*/*/*/*/*/${EXTRAS//,/-}/*.so*
-
- use doc && dohtml build/doc/rosetta++/docs/*
-
- cd bin || die
- for BIN in *; do
- newbin ${BIN} ${BIN%%.*} || die "could not install rosetta
program files"
- done
-
- if [[ -e "${ED}"/usr/bin/cluster ]]; then
- mv "${ED}"/usr/bin/cluster{,-${PN}} || die
- fi
-
- if [[ -e "${ED}"/usr/bin/benchmark ]]; then
- mv "${ED}"/usr/bin/benchmark{,-${PN}} || die
- fi
-}
-
-my_filter_option() {
- local value="$1"
- local exp="$2"
- local result=`echo ${value} | sed -e s/${exp}//g`
- echo "${result}"
- return 0;
-}
-
-my_list_append() {
- local old_value="$1"
- local new_value="$2"
- test -n "${old_value}" && old_value="${old_value},"
- echo "${old_value}${new_value}"
- return 0;
-}
