diff options
Diffstat (limited to 'sci-libs/libmems/files/libmems-1.6_p1-boost.patch')
| -rw-r--r-- | sci-libs/libmems/files/libmems-1.6_p1-boost.patch | 120 |
1 files changed, 120 insertions, 0 deletions
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>
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