diff options
Diffstat (limited to 'sci-libs/libmems')
| -rw-r--r-- | sci-libs/libmems/Manifest | 2 | ||||
| -rw-r--r-- | sci-libs/libmems/files/libmems-1.6_p1-boost.patch | 120 | ||||
| -rw-r--r-- | sci-libs/libmems/files/libmems-1.6_p1-build.patch | 19 | ||||
| -rw-r--r-- | sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch | 71 | ||||
| -rw-r--r-- | sci-libs/libmems/libmems-1.6.ebuild | 32 | ||||
| -rw-r--r-- | sci-libs/libmems/libmems-1.6_p1.ebuild | 32 | ||||
| -rw-r--r-- | sci-libs/libmems/libmems-9999.ebuild | 30 | ||||
| -rw-r--r-- | sci-libs/libmems/metadata.xml | 5 |
8 files changed, 311 insertions, 0 deletions
diff --git a/sci-libs/libmems/Manifest b/sci-libs/libmems/Manifest new file mode 100644 index 000000000000..c1c88d19ccc9 --- /dev/null +++ b/sci-libs/libmems/Manifest @@ -0,0 +1,2 @@ +DIST libmems-1.6.tar.bz2 441051 SHA256 624ef4921f00c2c81d179819a5d1af91f01b1ec66dfa5f7c977b8e42696e76b4 SHA512 4a4fdc2849c5e292175249834e702421c975b6fc5995c50abce90ad2e18df3a4fd0192330a0200dc18aa26bcce4de15baccd6f269555a7710dd4e620c0ca0738 WHIRLPOOL 4ea1cf8feca0a165dc970dc93e36a8602eb746ccb31bedfc20f960c9bb0c8268152f39b5725c6c917a2869df93d0539b518db4db4b43815172218f6620913cfe +DIST libmems-1.6_p1.tar.xz 226628 SHA256 c692d7d42378e7264d0a39674d1a6072183ee4c073ad90858153986b6a8b4848 SHA512 c6336f69b767bba010617deb2de9bb8fbbbaf516de3b1d293b062c76c6a763166080badd730938c6d849602d64a968edb6d4622b5d3e7ea7a6d8bc38164d3d73 WHIRLPOOL bc216dfb0c24c13b7b770da00100730e0e9b350c7bb6b312a480a83b51bc8c212e6ed73f08a88a7d262da8d4ed9a4c788883cbcfa3f2b2cdc362888e85b7f66a diff --git a/sci-libs/libmems/files/libmems-1.6_p1-boost.patch b/sci-libs/libmems/files/libmems-1.6_p1-boost.patch new file mode 100644 index 000000000000..4f0c775a6d9c --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-boost.patch @@ -0,0 +1,120 @@ + libMems/Backbone.cpp | 2 +- + libMems/Files.h | 64 +++++++++++++++++++++--------------------- + libMems/ProgressiveAligner.cpp | 2 +- + 3 files changed, 34 insertions(+), 34 deletions(-) + +diff --git a/libMems/Backbone.cpp b/libMems/Backbone.cpp +index 86698a9..0025cd8 100644 +--- a/libMems/Backbone.cpp ++++ b/libMems/Backbone.cpp +@@ -15,7 +15,7 @@ + #include "libMems/Islands.h"
+ #include "libMems/CompactGappedAlignment.h"
+
+-#include <boost/property_map.hpp>
++#include <boost/property_map/property_map.hpp>
+ #include <boost/graph/graph_traits.hpp>
+ #include <boost/graph/adjacency_list.hpp>
+ #include <boost/graph/topological_sort.hpp>
+diff --git a/libMems/Files.h b/libMems/Files.h +index 8d6e9be..8191065 100644 +--- a/libMems/Files.h ++++ b/libMems/Files.h +@@ -22,44 +22,44 @@ + + #include "boost/filesystem/operations.hpp" + #include "boost/filesystem/exception.hpp" +-#include "boost/algorithm/string.hpp"
++#include "boost/algorithm/string.hpp" + #include <string> + #include <sstream> + #include <iostream> + #include <iomanip> + + +-/**
+- * Register a file name to be deleted before the process exits
+- * When passed an empty string, it does not add to the list of files to delete
+- * @param fname The name of a file to delete, empty strings are ignored
+- * @return A vector of file names registered for deletion
+- */
+-std::vector< std::string >& registerFileToDelete( std::string fname = "" );
+-
+-inline
+-std::vector< std::string >& registerFileToDelete( std::string fname ) {
+- // since this vector is needed when atexit() is called we allocate it
+- // on the heap so its destructor won't get called
+- static std::vector< std::string >* files = new std::vector< std::string >();
+-#pragma omp critical
+-{
+- if( fname != "" )
+- files->push_back( fname );
+-}
+- return *files;
+-}
++/** ++ * Register a file name to be deleted before the process exits ++ * When passed an empty string, it does not add to the list of files to delete ++ * @param fname The name of a file to delete, empty strings are ignored ++ * @return A vector of file names registered for deletion ++ */ ++std::vector< std::string >& registerFileToDelete( std::string fname = "" ); + +-void deleteRegisteredFiles();
+-inline
+-void deleteRegisteredFiles() {
+- // don't be a slob, clean up after yourself:
+- // delete any files that are laying around
+- std::vector< std::string >& del_files = registerFileToDelete();
+- for( int fileI = 0; fileI < del_files.size(); fileI++ )
+- boost::filesystem::remove( del_files[ fileI ] );
+- del_files.clear(); // clear the deleted files from the list
+-}
++inline ++std::vector< std::string >& registerFileToDelete( std::string fname ) { ++ // since this vector is needed when atexit() is called we allocate it ++ // on the heap so its destructor won't get called ++ static std::vector< std::string >* files = new std::vector< std::string >(); ++#pragma omp critical ++{ ++ if( fname != "" ) ++ files->push_back( fname ); ++} ++ return *files; ++} ++ ++void deleteRegisteredFiles(); ++inline ++void deleteRegisteredFiles() { ++ // don't be a slob, clean up after yourself: ++ // delete any files that are laying around ++ std::vector< std::string >& del_files = registerFileToDelete(); ++ for( int fileI = 0; fileI < del_files.size(); fileI++ ) ++ boost::filesystem::remove( del_files[ fileI ] ); ++ del_files.clear(); // clear the deleted files from the list ++} + + + /** +@@ -80,7 +80,7 @@ std::string CreateTempFileName(const std::string& prefix) + #endif + boost::filesystem::path path( prefix ); + dir = path.branch_path().string(); +- name = path.leaf(); ++ name = path.filename().string(); + if( name == "/" ) + { + dir += name; +diff --git a/libMems/ProgressiveAligner.cpp b/libMems/ProgressiveAligner.cpp +index 3be5fe0..5667a9e 100644 +--- a/libMems/ProgressiveAligner.cpp ++++ b/libMems/ProgressiveAligner.cpp +@@ -27,7 +27,7 @@ +
+ #include <boost/dynamic_bitset.hpp>
+ #include <boost/tuple/tuple.hpp>
+-#include <boost/property_map.hpp>
++#include <boost/property_map/property_map.hpp>
+ #include <boost/graph/graph_traits.hpp>
+ #include <boost/graph/adjacency_list.hpp>
+ #include <boost/graph/johnson_all_pairs_shortest.hpp>
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-build.patch b/sci-libs/libmems/files/libmems-1.6_p1-build.patch new file mode 100644 index 000000000000..63e5f1216756 --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-build.patch @@ -0,0 +1,19 @@ + libMems/Makefile.am | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/libMems/Makefile.am b/libMems/Makefile.am +index 6101f71..d66053d 100644 +--- a/libMems/Makefile.am ++++ b/libMems/Makefile.am +@@ -2,10 +2,10 @@ + if DEBUG + D_CXXFLAGS = -Wall -g -D__GNDEBUG__ + endif +-OPTIMIZATION = -O2 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize + AM_CFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ -DUSE_POSIX_AIO @OPENMP_CFLAGS@ + AM_CXXFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ @BOOST_CPPFLAGS@ $(D_CXXFLAGS) @EXTRA_CXX_FLAGS@ @OPENMP_CXXFLAGS@ + AM_LDFLAGS = $(OPTIMIZATION) ++AM_CPPFLAGS=-I$(top_srcdir) + + LIBMEMS_H = \ + RepeatHash.h MatchHashEntry.h \ diff --git a/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch b/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch new file mode 100644 index 000000000000..ec620ebb35aa --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch @@ -0,0 +1,71 @@ + libMems/CompactGappedAlignment.h | 36 ++++++++++++++++++------------------ + 1 file changed, 18 insertions(+), 18 deletions(-) + +diff --git a/libMems/CompactGappedAlignment.h b/libMems/CompactGappedAlignment.h +index bf78477..942d4aa 100644 +--- a/libMems/CompactGappedAlignment.h ++++ b/libMems/CompactGappedAlignment.h +@@ -13,7 +13,7 @@ + #include "config.h"
+ #endif
+
+-#include "libGenome/gnDebug.h" ++#include "libGenome/gnDebug.h"
+ #include "libGenome/gnFilter.h"
+ #include "libGenome/gnSequence.h"
+ #include "libMems/SparseAbstractMatch.h"
+@@ -103,15 +103,15 @@ public: + /** Eliminates any columns that contain only gap characters */
+ void CondenseGapColumns();
+
+- void swap( CompactGappedAlignment& other ){ swap(&other); } +- +-protected: +- // for use by derived classes in order to swap contents +- void swap( CompactGappedAlignment* other ){ +- std::swap( align_matrix, other->align_matrix ); +- std::swap( bcount, other->bcount ); +- BaseType::swap( other ); +- } ++ void swap( CompactGappedAlignment& other ){ swap(&other); }
++
++protected:
++ // for use by derived classes in order to swap contents
++ void swap( CompactGappedAlignment* other ){
++ std::swap( align_matrix, other->align_matrix );
++ std::swap( bcount, other->bcount );
++ BaseType::swap( other );
++ }
+
+ std::vector< bitset_t > align_matrix; /**< aligned positions have true values, gaps are false */
+ std::vector< std::vector< size_t > > bcount;
+@@ -572,7 +572,7 @@ void CompactGappedAlignment<BaseType>::CropEnd(gnSeqI crop_amount){ + this->SetStart(i, 0);
+ }
+ }
+- SetAlignmentLength( this->AlignmentLength() - crop_amount );
++ this->SetAlignmentLength( this->AlignmentLength() - crop_amount );
+ this->create_bitcount();
+ if( !this->validate() )
+ std::cerr << "CropEnd error\n";
+@@ -806,13 +806,13 @@ void CompactGappedAlignment<BaseType>::CondenseGapColumns() +
+ }
+
+-namespace std { +-template<> inline +-void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b ) +-{ +- a.swap(b); +-} +-} ++namespace std {
++template<> inline
++void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b )
++{
++ a.swap(b);
++}
++}
+
+
+ #endif // __CompactGappedAlignment_h__
diff --git a/sci-libs/libmems/libmems-1.6.ebuild b/sci-libs/libmems/libmems-1.6.ebuild new file mode 100644 index 000000000000..56bb4be6dd7f --- /dev/null +++ b/sci-libs/libmems/libmems-1.6.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit autotools + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +IUSE="doc" +KEYWORDS="~amd64 ~x86" + +CDEPEND=" + dev-libs/boost + sci-libs/libgenome + sci-libs/libmuscle" +DEPEND="${CDEPEND} + doc? ( app-doc/doxygen )" +RDEPEND="${CDEPEND}" + +src_prepare() { + eautoreconf +} + +src_install() { + emake install DESTDIR="${D}" || die +} diff --git a/sci-libs/libmems/libmems-1.6_p1.ebuild b/sci-libs/libmems/libmems-1.6_p1.ebuild new file mode 100644 index 000000000000..c8d7dc9ecc92 --- /dev/null +++ b/sci-libs/libmems/libmems-1.6_p1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="doc" +KEYWORDS="~amd64 ~x86" + +CDEPEND=" + dev-libs/boost + sci-libs/libgenome + sci-libs/libmuscle" +DEPEND="${CDEPEND} + doc? ( app-doc/doxygen )" +RDEPEND="${CDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-build.patch + "${FILESDIR}"/${P}-boost.patch + "${FILESDIR}"/${P}-gcc-4.7.patch + ) diff --git a/sci-libs/libmems/libmems-9999.ebuild b/sci-libs/libmems/libmems-9999.ebuild new file mode 100644 index 000000000000..ff9052c10cfb --- /dev/null +++ b/sci-libs/libmems/libmems-9999.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +ESVN_REPO_URI="https://mauve.svn.sourceforge.net/svnroot/mauve/libMems/trunk" + +inherit autotools-utils subversion + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="" + +SLOT="0" +LICENSE="GPL-2" +IUSE="doc" +KEYWORDS="" + +CDEPEND=" + dev-libs/boost + sci-libs/libgenome + sci-libs/libmuscle" +DEPEND="${CDEPEND} + doc? ( app-doc/doxygen )" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}" diff --git a/sci-libs/libmems/metadata.xml b/sci-libs/libmems/metadata.xml new file mode 100644 index 000000000000..d4648212cbad --- /dev/null +++ b/sci-libs/libmems/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> |