diff options
Diffstat (limited to 'sci-libs/libmems/files')
7 files changed, 0 insertions, 293 deletions
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__
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