sci-libs/libmems: treeclean

Closes: https://bugs.gentoo.org/677558
Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>

11 files changed, 0 insertions, 392 deletions

diff --git a/sci-libs/libmems/Manifest b/sci-libs/libmems/Manifest
deleted file mode 100644
index b82404e2854c..000000000000
--- a/sci-libs/libmems/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST libmems-1.6_p1.tar.xz 226628 BLAKE2B 6410f8e0dc40855ce7a09127f4aa70face9007d5edbe424d595d8607a341137d8892008c5e6d9a37cbed05158d04b7d5a5ff5f02ba441b90cb30cbea2d21c88a SHA512 c6336f69b767bba010617deb2de9bb8fbbbaf516de3b1d293b062c76c6a763166080badd730938c6d849602d64a968edb6d4622b5d3e7ea7a6d8bc38164d3d73
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch b/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch
deleted file mode 100644
index 609d0de0c478..000000000000
--- a/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Shuffle around Boost type_traits, which otherwise causes issues with boost 1.62.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=595986
-
---- a/libMems/AbstractMatch.h
-+++ b/libMems/AbstractMatch.h
-@@ -16,8 +16,7 @@
- #include "libGenome/gnClone.h"

- #include <vector>

- #include <algorithm>

--#include <boost/type_traits/remove_pointer.hpp>

--#include <boost/type_traits/add_pointer.hpp>

-+#include <boost/type_traits.hpp>

- #include <boost/dynamic_bitset.hpp>

- #include <libMems/SlotAllocator.h>

- #include <libMems/configuration.h>

diff --git a/sci-libs/libmems/files/libmems-1.6_p1-boost.patch b/sci-libs/libmems/files/libmems-1.6_p1-boost.patch
deleted file mode 100644
index 4f0c775a6d9c..000000000000
--- a/sci-libs/libmems/files/libmems-1.6_p1-boost.patch
+++ /dev/null
@@ -1,120 +0,0 @@
- 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-broken-constness.patch b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch
deleted file mode 100644
index 0bd922c9e111..000000000000
--- a/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Fix bug 529770 caused by non-const copy constructor.
-
---- libmems-1.6_p1/libMems/Aligner.cpp
-+++ libmems-1.6_p1/libMems/Aligner.cpp
-@@ -939,7 +939,7 @@
- 	MatchLeftEndComparator( unsigned seq = 0 ){

- 		m_seq = seq;

- 	}

--	MatchLeftEndComparator( MatchLeftEndComparator& msc ){

-+	MatchLeftEndComparator( const MatchLeftEndComparator& msc ){

- 		m_seq = msc.m_seq;

- 	}

- 	// TODO??  make this do a wraparound comparison if all is equal?

---- libmems-1.6_p1/libMems/Aligner.h
-+++ libmems-1.6_p1/libMems/Aligner.h
-@@ -49,7 +49,7 @@
- 	LabeledMemComparator( uint seq ){

- 		m_seq = seq;

- 	}

--	LabeledMemComparator( LabeledMemComparator& lmc ){

-+	LabeledMemComparator( const LabeledMemComparator& lmc ){

- 		m_seq = lmc.m_seq;

- 	}

- 	boolean operator()(const LabeledMem& a, const LabeledMem& b) const{

diff --git a/sci-libs/libmems/files/libmems-1.6_p1-build.patch b/sci-libs/libmems/files/libmems-1.6_p1-build.patch
deleted file mode 100644
index 04d5dd9c82ac..000000000000
--- a/sci-libs/libmems/files/libmems-1.6_p1-build.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- 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 \
---- a/libMems/dmSML/util.c
-+++ b/libMems/dmSML/util.c
-@@ -2,6 +2,7 @@
- #include "config.h"
- #endif
- 
-+#include <stdlib.h>
- #include <stdio.h>
- #include "libMems/dmSML/util.h"
- 
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch
deleted file mode 100644
index bde8efeb4c9c..000000000000
--- a/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Description: Correct compilation with g++-6
-Author: Gert Wollny <gw.fossdev@gmail.com>
-Bug-Debian: https://bugs.debian.org/811870
-Forwarded: yes
-Bug: https://sourceforge.net/p/mauve/bugs/46/
-Last-Update: 2016-06-30
-
---- a/libMems/ProgressiveAligner.cpp
-+++ b/libMems/ProgressiveAligner.cpp
-@@ -1599,7 +1599,7 @@
- 		c.SetLeftEnd(child_1, ancestral_matches[mI]->LeftEnd(1));

- 		c.SetOrientation(child_1, ancestral_matches[mI]->Orientation(1));

- 		c.SetLength(ancestral_matches[mI]->Length(1), child_1);

--		cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));

-+		cga_list.push_back(boost::tuples::make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));

- 	}

- 

- 	stack<node_id_t> node_stack;

diff --git a/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch b/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch
deleted file mode 100644
index 3ad3da2a8d80..000000000000
--- a/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- libMems/dmSML/dmsort.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/libMems/dmSML/dmsort.c b/libMems/dmSML/dmsort.c
-index 4c99215..2cbfa7e 100644
---- a/libMems/dmSML/dmsort.c
-+++ b/libMems/dmSML/dmsort.c
-@@ -825,7 +825,7 @@ int InitdmSML( long working_mb, long buffer_size, const char* input_filename, co
- 		if ( fgets(buf, sizeof(buf), fp) )
- 		{
- 			sscanf(buf, "MemTotal: %ld kB", &memTotal);
--			fprintf( stderr, buf );
-+			fprintf( stderr, "%s", buf );
- 		}
- 		fclose(fp);
- 		// allocate about 6/10 of physical memory
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
deleted file mode 100644
index ec620ebb35aa..000000000000
--- a/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch
+++ /dev/null
@@ -1,71 +0,0 @@
- 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_p1-r3.ebuild b/sci-libs/libmems/libmems-1.6_p1-r3.ebuild
deleted file mode 100644
index 513fd1f3af61..000000000000
--- a/sci-libs/libmems/libmems-1.6_p1-r3.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="Library for sci-biology/mauve"
-HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="GPL-2"
-IUSE="doc static-libs"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-libs/boost:=
-	sci-libs/libgenome
-	sci-libs/libmuscle"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-build.patch
-	"${FILESDIR}"/${P}-boost.patch
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${P}-broken-constness.patch
-	"${FILESDIR}"/${P}-format-security.patch
-	"${FILESDIR}"/${P}-fix-c++14.patch
-	"${FILESDIR}"/${P}-boost-1.62-type-traits.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--enable-shared \
-		$(use_enable static-libs static)
-}
-
-src_compile() {
-	default
-
-	if use doc; then
-		doxygen doxygen.am || die
-		HTML_DOCS+=( html/. )
-	fi
-}
-
-src_install() {
-	default
-
-	# package provides .pc files
-	find "${D}" -name '*.la' -delete || die
-}
diff --git a/sci-libs/libmems/libmems-9999.ebuild b/sci-libs/libmems/libmems-9999.ebuild
deleted file mode 100644
index 782686270355..000000000000
--- a/sci-libs/libmems/libmems-9999.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools subversion
-
-DESCRIPTION="Library for sci-biology/mauve"
-HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
-SRC_URI=""
-ESVN_REPO_URI="https://svn.code.sf.net/p/mauve/code/libMems/trunk"
-
-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}"
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-libs/libmems/metadata.xml b/sci-libs/libmems/metadata.xml
deleted file mode 100644
index bdabd1d83788..000000000000
--- a/sci-libs/libmems/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>