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sci-biology/vaal: Remove old patches
Package-Manager: portage-2.2.26
This commit is contained in:
Ted Tanberry
@@ -1,22 +0,0 @@
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--- VAAL.orig/MakeDepend.cc 2008-12-18 17:05:48.000000000 +0100
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+++ VAAL/MakeDepend.cc 2010-02-14 13:42:23.734370178 +0100
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@@ -1195,9 +1195,6 @@
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}
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}
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mf << " -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)";
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- for ( set<string>::iterator dep_iter = lib_deps.begin();
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- dep_iter != lib_deps.end(); ++dep_iter )
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- mf << " " << "$(" << *dep_iter << "_LFLAGS)";
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for ( set<string>::iterator dep_iter = sharedlib_deps.begin();
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dep_iter != sharedlib_deps.end(); ++dep_iter ) {
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// Extract the symbolic name of this library from its filename.
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@@ -1208,6 +1205,9 @@
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mf << " -l" << sharedlib_name;
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}
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mf << " -l" << libname;
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+ for ( set<string>::iterator dep_iter = lib_deps.begin();
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+ dep_iter != lib_deps.end(); ++dep_iter )
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+ mf << " " << "$(" << *dep_iter << "_LFLAGS)";
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mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
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}
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}
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@@ -1,39 +0,0 @@
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diff -durr VAAL.orig/SortKmersImpl.h VAAL/SortKmersImpl.h
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--- VAAL.orig/SortKmersImpl.h 2009-11-12 13:02:40.116993289 +0000
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+++ VAAL/SortKmersImpl.h 2009-11-12 13:04:59.416388534 +0000
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@@ -98,7 +98,7 @@
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{ if ( reads[l].size( ) < KSPAN ) continue;
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unsigned int N = reads[l].size( ) - KSPAN + 1;
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if ( S + 2*N >= R.size( ) ) {
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- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
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+ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
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if ( nn < R.size( ) ) FatalErr( "SortKmers<1>: Unsigned-int overflow (R=" << R.size( ) << ")" );
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R.resize(nn);
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}
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@@ -180,7 +180,7 @@
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}
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if ( q == N ) break;
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if ( S + 2*N >= R.size( ) ) {
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- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
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+ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
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if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
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R.resize(nn);
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}
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@@ -207,7 +207,7 @@
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top += Min( N - top, (unsigned int) 10000 );
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if ( S + 20000 >= R.size( ) || S + 2*N >= R.size( ) ) {
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- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
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+ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
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if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
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R.resize(nn);
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}
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@@ -318,7 +318,7 @@
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top += Min( N - top, 10000 );
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if ( S + 2*(top - q) >= R.size( ) ) {
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- unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (S + 2*(top - q)) );
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+ unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (unsigned) (S + 2*(top - q)) );
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if ( nn < R.size( ) ) FatalErr( "SortKmers<100>: Unsigned-int overflow (R=" << R.size( ) << ")" );
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R.resize(nn);
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}
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@@ -1,60 +0,0 @@
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--- VAAL.orig/Makefile.in 2009-04-02 21:43:42.000000000 +0200
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+++ VAAL/Makefile.in 2010-02-14 14:20:26.222370302 +0100
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@@ -161,12 +161,16 @@
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COMPILER = @CC@
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CPLUSPLUS = @CXX@
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+CFLAGS = @CFLAGS@
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+CXXFLAGS = @CXXFLAGS@
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+LDFLAGS = @LDFLAGS@
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+
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# QUIET=yes causes the compiler to be less verbose about warnings.
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QUIET = no
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# DEBUG=yes forces out-of-date executables to be built with symbolic
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# debugging information. Any other value is ignored.
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-DEBUG = yes
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+DEBUG = no
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# OPTIM=<compiler optimization> forces user-defined optimizations to be used,
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# rather than the compiler-specific default.
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@@ -174,7 +178,7 @@
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# If OPTIM=none, then no optimization is used.
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# If unset, defaults are used.
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# -fno-exceptions
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-OPTIM =
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+OPTIM = none
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# PROFILE=yes builds sampled-profiling (i.e. gprof) executables. Any other
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# value is ignored.
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@@ -317,6 +321,7 @@
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# Setup final compilation options:
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CPP_OPTIONS = \
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+ $(CXXFLAGS) \
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$(SYS_WARN) \
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$(SYS_OPT) \
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$(SYS_DEBUG) \
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@@ -328,6 +333,7 @@
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@INCLUDES@
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LINK_OPTIONS = \
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+ $(LDFLAGS) \
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$(SYS_DEBUG) \
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$(SYS_LINK) \
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$(OMP_LINK) \
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@@ -406,12 +406,12 @@
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$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
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checkLock: $(SRC)/util/checkLock.cc
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- $(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock
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+ $(CPLUSPLUS) $(CXXFLAGS) $(SRC)/util/checkLock.cc $(LDFLAGS) -o $(BIN)/checkLock
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random/Random.o: random/Random.cc
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@ mkdir -p $(OBJ)/${@D}
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cp $(SRC)/random/Random.cc $(SRC)/random/Random.c
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- $(CC) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
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+ $(CC) $(CFLAGS) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
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rm $(SRC)/random/Random.c
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MemTracker.o: MemTracker.cc
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@@ -1,153 +0,0 @@
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Fix building with gcc-4.7
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https://bugs.gentoo.org/show_bug.cgi?id=423497
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Patch written by Kacper Kowalik <xarthisius@gentoo.org>
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--- a/src/feudal/MasterVec.h
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+++ b/src/feudal/MasterVec.h
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@@ -62,20 +62,20 @@
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/// This function is deprecated: Use reserve() instead.
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/// The pool size argument is ignored, anyway.
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MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity )
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- { reserve(capacity); return *this; }
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+ { this->reserve(capacity); return *this; }
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/// This function is deprecated: Use clear().shrink_to_fit().
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MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; }
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/// This function is deprecated: Use push_back().
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MasterVec& push_back_external( T const& val )
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- { push_back(val); return *this; }
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+ { this->push_back(val); return *this; }
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/// This function is deprecated: Use push_back().
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MasterVec& push_back_reserve( T const& val,
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size_type growthIncr = 0,
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float growthFact = 1.3f )
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- { push_back(val,growthFact,growthIncr); return *this; }
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+ { this->push_back(val,growthFact,growthIncr); return *this; }
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/// This function is deprecated: Use append().
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MasterVec& Append( MasterVec const& that )
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@@ -83,7 +83,7 @@
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/// This function is deprecated: Use append().
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MasterVec& Append( MasterVec const& that, size_type from, size_type to )
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- { append(that.begin(from),that.begin(to)); return *this; }
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+ { this->append(that.begin(from),that.begin(to)); return *this; }
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MasterVec const& WriteAll( String const& fileName ) const
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{ return WriteRange(fileName,0UL,BaseT::size()); return *this; }
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@@ -108,7 +108,7 @@
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{ if ( !append ) BaseT::clear();
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FeudalFileReader rdr(fileName.c_str());
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size_type siz = rdr.getNElements();
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- reserve(BaseT::size()+siz);
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+ this->reserve(BaseT::size()+siz);
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preAlloc(rdr,0,siz);
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for ( size_type iii = 0; iii < siz; ++iii )
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appendFromReader(rdr,iii);
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--- a/src/feudal/FeudalControlBlock.cc
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+++ b/src/feudal/FeudalControlBlock.cc
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@@ -24,6 +24,7 @@
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#include <string.h>
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#include <errno.h>
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#include <iostream>
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+#include <unistd.h>
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using std::cout;
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using std::endl;
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--- a/src/feudal/SerfVec.h
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+++ b/src/feudal/SerfVec.h
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@@ -83,9 +83,9 @@
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{ AssertLe(pos,that.size());
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AssertLe(len,that.size()-pos);
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if ( this != &that )
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- { assign(that.begin(pos),that.begin(pos+len)); }
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+ { this->assign(that.begin(pos),that.begin(pos+len)); }
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else
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- { erase(BaseT::begin(),BaseT::begin(pos));
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+ { this->erase(BaseT::begin(),BaseT::begin(pos));
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BaseT::resize(len); }
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return *this; }
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--- a/src/system/ProcBuf.cc
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+++ b/src/system/ProcBuf.cc
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@@ -195,12 +195,12 @@
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Assert(M_internal_put_buffer == NULL);
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M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE];
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M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE;
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- setp(M_internal_put_buffer,
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+ this->setp(M_internal_put_buffer,
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M_internal_put_buffer_end);
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} else if (!flush())
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return traits_type::eof();
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if (!traits_type::eq_int_type(c, traits_type::eof()))
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- return sputc(c);
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+ return this->sputc(c);
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else
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return traits_type::not_eof(c);
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}
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@@ -240,7 +240,7 @@
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// (which is start of buffer)
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std::copy_backward(this->eback(), this->egptr(), this->egptr()+1);
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*(this->gptr()) = traits_type::to_char_type(c);
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- setg(this->eback(), this->gptr(), this->egptr()+1);
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+ this->setg(this->eback(), this->gptr(), this->egptr()+1);
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return traits_type::not_eof(c);
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} else
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return traits_type::eof();
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@@ -269,7 +269,7 @@
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// doing wchars and we write an odd # of bytes?
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return false;
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} else {
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- setp(this->pbase(), this->epptr());
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+ this->setp(this->pbase(), this->epptr());
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return true;
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}
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}
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@@ -283,7 +283,7 @@
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Assert(M_internal_get_buffer == NULL);
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M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE];
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M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE;
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- setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
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+ this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
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}
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// The "get" pointer should be at the end of the buffer - that's
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// why we need to fill it.
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@@ -318,7 +318,7 @@
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//
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// reset the get pointers
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//
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- setg(M_internal_get_buffer,
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+ this->setg(M_internal_get_buffer,
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M_internal_get_buffer,
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M_internal_get_buffer+numusable/sizeof(char_type));
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return true;
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--- a/src/system/SysConf.cc
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+++ b/src/system/SysConf.cc
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@@ -19,6 +19,7 @@
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#include "system/SysConf.h"
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#include "system/Exit.h"
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#include <iostream>
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+#include <unistd.h>
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namespace
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{
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--- a/src/Vec.h
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+++ b/src/Vec.h
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@@ -261,11 +261,11 @@
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template <class U>
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void append( const vec<U>& y )
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- { insert( this->end( ), y.begin( ), y.end( ) ); }
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+ { this->insert( this->end( ), y.begin( ), y.end( ) ); }
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void append( const vec<T>& y, size_type i, size_type j ) {
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- if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) );
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- else insert( this->end( ), y.begin( ) + i, y.begin( ) + j );
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+ if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) );
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+ else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j );
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}
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// appends values in y, but only those whose indices are in entries
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@@ -1,12 +0,0 @@
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diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac
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--- vaal-33805.orig/configure.ac 2010-09-20 04:37:49.858059826 +0000
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+++ vaal-33805/configure.ac 2010-09-20 04:39:41.178059477 +0000
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@@ -14,7 +14,7 @@
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AC_OPENMP
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AC_OPENMP_CEHCK
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-CXXFLAGS=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
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+CXXFLAGS+=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
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OS_RELEASE="`uname -r`"
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AC_SUBST(CXXFLAGS)
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