commit: 858d99d15749bcb2aa8359f295946cf26179ede5 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Mon Aug 3 13:21:31 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Aug 3 13:21:31 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=858d99d1
sci-chemistry/rosetta: Add patch for boost-1.57 and add support for gcc-4.9 Package-Manager: portage-2.2.20 sci-chemistry/rosetta/ChangeLog | 8 ++++-- .../rosetta/files/rosetta-3.4-boost157.patch | 16 +++++++++++ .../rosetta/files/rosetta-3.4-gcc4.789.patch | 32 ++++++++++++++++++++++ sci-chemistry/rosetta/metadata.xml | 20 +++++++------- sci-chemistry/rosetta/rosetta-3.4.ebuild | 5 ++-- 5 files changed, 67 insertions(+), 14 deletions(-) diff --git a/sci-chemistry/rosetta/ChangeLog b/sci-chemistry/rosetta/ChangeLog index 89adc6e..bfe7b09 100644 --- a/sci-chemistry/rosetta/ChangeLog +++ b/sci-chemistry/rosetta/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-chemistry/rosetta -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 03 Aug 2015; Justin Lecher <[email protected]> + +files/rosetta-3.4-boost157.patch, +files/rosetta-3.4-gcc4.789.patch, + metadata.xml, rosetta-3.4.ebuild: + sci-chemistry/rosetta: Add patch for boost-1.57 and add support for gcc-4.9 + 11 Jun 2013; Justin Lecher <[email protected]> rosetta-3.4.ebuild: Fix: Ebuild calls die in a subshell @@ -58,4 +63,3 @@ Thanks to Hugo Mildenberger for intial ebuild BOINC support is broken because current version of libboinc_zip.a sucks (TEXTREL, not compiled w/ fPIC) - diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch b/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch new file mode 100644 index 0000000..c2d7594 --- /dev/null +++ b/sci-chemistry/rosetta/files/rosetta-3.4-boost157.patch @@ -0,0 +1,16 @@ + 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-gcc4.789.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.patch new file mode 100644 index 0000000..e11532a --- /dev/null +++ b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.789.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", "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/metadata.xml b/sci-chemistry/rosetta/metadata.xml index f122201..79c6e95 100644 --- a/sci-chemistry/rosetta/metadata.xml +++ b/sci-chemistry/rosetta/metadata.xml @@ -1,14 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> -<herd>sci-chemistry</herd> - <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>[email protected]</bugs-to> - </upstream> + <herd>sci-chemistry</herd> + <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>[email protected]</bugs-to> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild index 4a0acc1..e0a0772 100644 --- a/sci-chemistry/rosetta/rosetta-3.4.ebuild +++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -63,7 +63,8 @@ src_prepare() { "${FILESDIR}"/${P}-fix-valgrind.patch \ "${FILESDIR}"/${P}-boinc.patch \ "${FILESDIR}"/${P}-boost.patch \ - "${FILESDIR}"/${P}-gcc4.78.patch + "${FILESDIR}"/${P}-boost157.patch \ + "${FILESDIR}"/${P}-gcc4.789.patch eprefixify tools/build/*
