Merge branch 'SoapZaNet-bug-568438'

* SoapZaNet-bug-568438: sci-biology/vaal: Remove old patches sci-biology/vaal: Gentoo-Bug: 568438, fix global namespace std:: clash.
2026-08-05 12:38:09 -07:00 · 2015-12-27 17:34:31 +01:00
parent 923170efdf e4e2a2eb17
commit a32dafa1ef
7 changed files with 953 additions and 286 deletions
--- a/sci-biology/vaal/files/vaal-1.2-as-needed.patch
+++ b/sci-biology/vaal/files/vaal-1.2-as-needed.patch
@@ -1,22 +0,0 @@
--- VAAL.orig/MakeDepend.cc	2008-12-18 17:05:48.000000000 +0100
-+++ VAAL/MakeDepend.cc	2010-02-14 13:42:23.734370178 +0100
-@@ -1195,9 +1195,6 @@
-       }
-     }
-     mf << " -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; 
-    for ( set<string>::iterator dep_iter = lib_deps.begin(); 
-	  dep_iter != lib_deps.end(); ++dep_iter )
-      mf << " " << "$(" << *dep_iter << "_LFLAGS)";
-     for ( set<string>::iterator dep_iter = sharedlib_deps.begin();
-           dep_iter != sharedlib_deps.end(); ++dep_iter ) {
-       // Extract the symbolic name of this library from its filename.
-@@ -1208,6 +1205,9 @@
-       mf << " -l" << sharedlib_name;
-     }
-     mf << " -l" << libname;
-+    for ( set<string>::iterator dep_iter = lib_deps.begin(); 
-+	  dep_iter != lib_deps.end(); ++dep_iter )
-+      mf << " " << "$(" << *dep_iter << "_LFLAGS)";
-     mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
-   }
- }    
--- a/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch
+++ b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch
@@ -1,39 +0,0 @@
-diff -durr VAAL.orig/SortKmersImpl.h VAAL/SortKmersImpl.h
--- VAAL.orig/SortKmersImpl.h	2009-11-12 13:02:40.116993289 +0000
-+++ VAAL/SortKmersImpl.h	2009-11-12 13:04:59.416388534 +0000
-@@ -98,7 +98,7 @@
-     {    if ( reads[l].size( ) < KSPAN ) continue;
-     unsigned int N = reads[l].size( ) - KSPAN + 1;
-     if ( S + 2*N >= R.size( ) ) {
-      unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
-+      unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
-       if ( nn < R.size( ) ) FatalErr( "SortKmers<1>: Unsigned-int overflow (R=" << R.size( ) << ")" );
-       R.resize(nn);
-     }
-@@ -180,7 +180,7 @@
- 	}
- 	if ( q == N ) break;
- 	if ( S + 2*N >= R.size( ) ) {
-	  unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
-+	  unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
- 	  if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
- 	  R.resize(nn);
- 	}
-@@ -207,7 +207,7 @@
-       top += Min( N - top, (unsigned int) 10000 );
-       
-       if ( S + 20000 >= R.size( ) || S + 2*N >= R.size( ) ) {
-	unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
-+	unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
- 	if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
- 	R.resize(nn);
-       }
-@@ -318,7 +318,7 @@
- 
- 	  top += Min( N - top, 10000 );
- 	  if ( S + 2*(top - q) >= R.size( ) ) {
-	    unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (S + 2*(top - q)) );
-+	    unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (unsigned) (S + 2*(top - q)) );
- 	    if ( nn < R.size( ) ) FatalErr( "SortKmers<100>: Unsigned-int overflow (R=" << R.size( ) << ")" );
- 	    R.resize(nn);
- 	  }
--- a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
+++ b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
@@ -1,60 +0,0 @@
--- VAAL.orig/Makefile.in	2009-04-02 21:43:42.000000000 +0200
-+++ VAAL/Makefile.in	2010-02-14 14:20:26.222370302 +0100
-@@ -161,12 +161,16 @@
- COMPILER	= @CC@
- CPLUSPLUS	= @CXX@
- 
-+CFLAGS		= @CFLAGS@
-+CXXFLAGS	= @CXXFLAGS@
-+LDFLAGS 	= @LDFLAGS@
-+
- # QUIET=yes causes the compiler to be less verbose about warnings.
- QUIET		= no
- 
- # DEBUG=yes forces out-of-date executables to be built with symbolic
- # debugging information.  Any other value is ignored.
-DEBUG		= yes
-+DEBUG		= no
- 
- # OPTIM=<compiler optimization> forces user-defined optimizations to be used,
- # rather than the compiler-specific default.  
-@@ -174,7 +178,7 @@
- # If OPTIM=none, then no optimization is used.	
- # If unset, defaults are used.
- # -fno-exceptions
-OPTIM		= 
-+OPTIM		= none
- 
- # PROFILE=yes builds sampled-profiling (i.e. gprof) executables. Any other
- # value is ignored.
-@@ -317,6 +321,7 @@
- # Setup final compilation options:
- 
- CPP_OPTIONS	= \
-+		$(CXXFLAGS) \
- 		$(SYS_WARN) \
- 		$(SYS_OPT) \
- 		$(SYS_DEBUG) \
-@@ -328,6 +333,7 @@
- 		@INCLUDES@
- 
- LINK_OPTIONS	= \
-+		$(LDFLAGS) \
- 		$(SYS_DEBUG) \
- 		$(SYS_LINK) \
- 		$(OMP_LINK) \
-@@ -406,12 +406,12 @@
- 	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
- 
- checkLock: $(SRC)/util/checkLock.cc
-	$(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock 
-+	$(CPLUSPLUS) $(CXXFLAGS) $(SRC)/util/checkLock.cc $(LDFLAGS) -o $(BIN)/checkLock 
- 
- random/Random.o: random/Random.cc
- 	@ mkdir -p $(OBJ)/${@D}
- 	cp $(SRC)/random/Random.cc $(SRC)/random/Random.c
-	$(CC) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
-+	$(CC) $(CFLAGS) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o
- 	rm $(SRC)/random/Random.c
- 
- MemTracker.o: MemTracker.cc
--- a/sci-biology/vaal/files/vaal-1.6-gcc47.patch
+++ b/sci-biology/vaal/files/vaal-1.6-gcc47.patch
@@ -1,153 +0,0 @@
-Fix building with gcc-4.7
-
-https://bugs.gentoo.org/show_bug.cgi?id=423497
-
-Patch written by Kacper Kowalik <xarthisius@gentoo.org>
--- a/src/feudal/MasterVec.h
-+++ b/src/feudal/MasterVec.h
-@@ -62,20 +62,20 @@
-     /// This function is deprecated: Use reserve() instead.
-     /// The pool size argument is ignored, anyway.
-     MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity )
-    { reserve(capacity); return *this; }
-+    { this->reserve(capacity); return *this; }
- 
-     /// This function is deprecated:  Use clear().shrink_to_fit().
-     MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; }
- 
-     /// This function is deprecated:  Use push_back().
-     MasterVec& push_back_external( T const& val )
-    { push_back(val); return *this; }
-+    { this->push_back(val); return *this; }
- 
-     /// This function is deprecated:  Use push_back().
-     MasterVec& push_back_reserve( T const& val,
-                                   size_type growthIncr = 0,
-                                   float growthFact = 1.3f )
-    { push_back(val,growthFact,growthIncr); return *this; }
-+    { this->push_back(val,growthFact,growthIncr); return *this; }
- 
-     /// This function is deprecated:  Use append().
-     MasterVec& Append( MasterVec const& that )
-@@ -83,7 +83,7 @@
- 
-     /// This function is deprecated:  Use append().
-     MasterVec& Append( MasterVec const& that, size_type from, size_type to )
-    { append(that.begin(from),that.begin(to)); return *this; }
-+    { this->append(that.begin(from),that.begin(to)); return *this; }
- 
-     MasterVec const& WriteAll( String const& fileName ) const
-     { return WriteRange(fileName,0UL,BaseT::size()); return *this; }
-@@ -108,7 +108,7 @@
-     { if ( !append ) BaseT::clear();
-       FeudalFileReader rdr(fileName.c_str());
-       size_type siz = rdr.getNElements();
-      reserve(BaseT::size()+siz);
-+      this->reserve(BaseT::size()+siz);
-       preAlloc(rdr,0,siz);
-       for ( size_type iii = 0; iii < siz; ++iii )
-         appendFromReader(rdr,iii);
--- a/src/feudal/FeudalControlBlock.cc
-+++ b/src/feudal/FeudalControlBlock.cc
-@@ -24,6 +24,7 @@
- #include <string.h>
- #include <errno.h>
- #include <iostream>
-+#include <unistd.h>
- 
- using std::cout;
- using std::endl;
--- a/src/feudal/SerfVec.h
-+++ b/src/feudal/SerfVec.h
-@@ -83,9 +83,9 @@
-     { AssertLe(pos,that.size());
-       AssertLe(len,that.size()-pos);
-       if ( this != &that )
-      { assign(that.begin(pos),that.begin(pos+len)); }
-+      { this->assign(that.begin(pos),that.begin(pos+len)); }
-       else
-      { erase(BaseT::begin(),BaseT::begin(pos));
-+      { this->erase(BaseT::begin(),BaseT::begin(pos));
-         BaseT::resize(len); }
-       return *this; }
- 
--- a/src/system/ProcBuf.cc
-+++ b/src/system/ProcBuf.cc
-@@ -195,12 +195,12 @@
- 	    Assert(M_internal_put_buffer == NULL);
- 	    M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE];
- 	    M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE;
-	    setp(M_internal_put_buffer,
-+	    this->setp(M_internal_put_buffer,
- 		 M_internal_put_buffer_end);
- 	} else if (!flush())
- 	    return traits_type::eof();
- 	if (!traits_type::eq_int_type(c, traits_type::eof()))
-	    return sputc(c);
-+	    return this->sputc(c);
- 	else
- 	    return traits_type::not_eof(c);
-     }
-@@ -240,7 +240,7 @@
- 	// (which is start of buffer)
- 	std::copy_backward(this->eback(), this->egptr(), this->egptr()+1);
- 	*(this->gptr()) = traits_type::to_char_type(c);
-	setg(this->eback(), this->gptr(), this->egptr()+1);
-+	this->setg(this->eback(), this->gptr(), this->egptr()+1);
-         return traits_type::not_eof(c);
-     } else
- 	return traits_type::eof();
-@@ -269,7 +269,7 @@
- 	// doing wchars and we write an odd # of bytes?
- 	return false;
-     } else {
-	setp(this->pbase(), this->epptr());
-+	this->setp(this->pbase(), this->epptr());
- 	return true;
-     }
- }
-@@ -283,7 +283,7 @@
- 	Assert(M_internal_get_buffer == NULL);
- 	M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE];
- 	M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE;
-	setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
-+	this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
-     }
-     // The "get" pointer should be at the end of the buffer - that's
-     // why we need to fill it.
-@@ -318,7 +318,7 @@
-     //
-     // reset the get pointers
-     //
-    setg(M_internal_get_buffer, 
-+    this->setg(M_internal_get_buffer, 
- 	 M_internal_get_buffer, 
- 	 M_internal_get_buffer+numusable/sizeof(char_type));
-     return true;
--- a/src/system/SysConf.cc
-+++ b/src/system/SysConf.cc
-@@ -19,6 +19,7 @@
- #include "system/SysConf.h"
- #include "system/Exit.h"
- #include <iostream>
-+#include <unistd.h>
- 
- namespace
- {
--- a/src/Vec.h
-+++ b/src/Vec.h
-@@ -261,11 +261,11 @@
- 
-   template <class U>
-   void append( const vec<U>& y ) 
-  {    insert( this->end( ), y.begin( ), y.end( ) );    }
-+  {    this->insert( this->end( ), y.begin( ), y.end( ) );    }
-   
-   void append( const vec<T>& y, size_type i, size_type j ) {
-    if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) );
-    else insert( this->end( ), y.begin( ) + i, y.begin( ) + j );   
-+    if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) );
-+    else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j );   
-   }
- 
-   // appends values in y, but only those whose indices are in entries
--- a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
+++ b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
@@ -1,12 +0,0 @@
-diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac
--- vaal-33805.orig/configure.ac	2010-09-20 04:37:49.858059826 +0000
-+++ vaal-33805/configure.ac	2010-09-20 04:39:41.178059477 +0000
-@@ -14,7 +14,7 @@
- AC_OPENMP
- AC_OPENMP_CEHCK
- 
-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 ."
-+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 ."
- 
- OS_RELEASE="`uname -r`"
- AC_SUBST(CXXFLAGS)
--- a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
+++ b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch
@@ -0,0 +1,911 @@
+Remove 'using namespace std' causing massive havoc with newly
+introduced std::align in GCC-5. Fix bug
+https://bugs.gentoo.org/show_bug.cgi?id=568438
+
+--- vaal-46233/src/efasta/EfastaTools.cc
+++ vaal-46233/src/efasta/EfastaTools.cc
+@@ -18,6 +18,8 @@
+ #include "math/Functions.h"
+ #include "math/Array.h"
+ 
+using std::set;
+
+ #define Err(message)                                      \
+ {    cout << message << endl << "\nInvalid.\n" << endl;   \
+      TracebackThisProcess( );    }
+--- vaal-46233/src/Equiv.cc
+++ vaal-46233/src/Equiv.cc
+@@ -9,6 +9,8 @@
+ #include "Equiv.h"
+ #include "Vec.h"
+ 
+using std::swap;
+
+ bool equivalence_relation::equiv(int a, int b) const
+ {    if ( a == b ) return true;
+      int c = a;
+--- vaal-46233/src/FastaFilestream.cc
+++ vaal-46233/src/FastaFilestream.cc
+@@ -13,6 +13,8 @@
+ 
+ #include <strstream>
+ 
+using std::string;
+
+ template <typename vecT, typename seqT, typename convT, typename verifT>
+ FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename,
+                                                           FastaNameParser* name_parser )
+--- vaal-46233/src/FastaFilestreamPreview.cc
+++ vaal-46233/src/FastaFilestreamPreview.cc
+@@ -11,6 +11,8 @@
+ 
+ #include <algorithm>
+ 
+using std::streamoff;
+
+ FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream)
+   : max_sequence_size_(0), start_offset_(0)
+ {
+--- vaal-46233/src/FastaFilestreamPreview.h
+++ vaal-46233/src/FastaFilestreamPreview.h
+@@ -12,6 +12,8 @@
+ 
+ #include "Vec.h"
+ 
+using std::streampos;
+
+ // FastaFilestreamPreview understands just enough about the fasta
+ // format to be able to count the number of sequences in the specified
+ // filestream and to know where each sequence starts in that filestream.
+--- vaal-46233/src/Fastavector.cc
+++ vaal-46233/src/Fastavector.cc
+@@ -14,6 +14,8 @@
+ #include <istream>
+ #include <string>
+ 
+using std::max;
+
+ // Split this into chunks, separated by gaps ('n'), and return each chunk as a
+ // gapless fastavector.
+ // TODO: generalize this into a templatized STL algorithm.
+--- vaal-46233/src/Fastavector.h
+++ vaal-46233/src/Fastavector.h
+@@ -24,6 +24,9 @@
+ #include <iostream>
+ #include <unistd.h>
+ 
+using std::string;
+using std::istringstream;
+
+ typedef std::tuple<String, int, int> FastaRegion;
+ 
+ class fastaindex {
+--- vaal-46233/src/FetchReads.cc
+++ vaal-46233/src/FetchReads.cc
+@@ -36,6 +36,8 @@
+ #include "Qualvector.h"
+ #include "random/Random.h"
+ 
+using std::istringstream;
+
+ // Heuristic constants:
+ 
+ namespace
+--- vaal-46233/src/feudal/BaseVec.cc
+++ vaal-46233/src/feudal/BaseVec.cc
+@@ -21,6 +21,7 @@
+ using std::ostream;
+ using std::cout;
+ using std::endl;
+using std::max_element;
+ 
+ // Cap: in a given basevector, replace any sequence of N > n identical
+ // bases by n of the same base.
+--- vaal-46233/src/graph/Digraph.cc
+++ vaal-46233/src/graph/Digraph.cc
+@@ -16,6 +16,8 @@
+ #include "graph/Digraph.h"
+ #include "math/Functions.h"
+ 
+using std::make_pair;
+
+ Bool digraph::HasEdge( int v, int w ) const {
+   return find( from_[v].begin(),  from_[v].end(), w ) != from_[v].end();
+ }
+--- vaal-46233/src/graph/DigraphTemplate.h
+++ vaal-46233/src/graph/DigraphTemplate.h
+@@ -34,6 +34,8 @@
+ #include "graph/Digraph.h"
+ #include <cstddef>
+ 
+using std::make_pair;
+
+ template<class E> vec<int> digraphE<E>::EdgesConnectedTo( const vec<int>& v ) const
+ {    vec<int> G = VerticesConnectedTo(v), e;
+      for ( int x = 0; x < G.isize( ); x++ )
+--- vaal-46233/src/IndexedAlignmentPlusVector.cc
+++ vaal-46233/src/IndexedAlignmentPlusVector.cc
+@@ -9,6 +9,8 @@
+ #include "IndexedAlignmentPlusVector.h"
+ #include "VecAlignmentPlus.h"
+ 
+using std::streamoff;
+
+ // These strings are at the head of the vector and index files for verification purposes.
+ 
+ const String VecAlignmentPlusHeaderIO::mStrVectorHeader( "alignment_plus vector V.2\n" );
+--- vaal-46233/src/IndexedAlignmentPlusVector.h
+++ vaal-46233/src/IndexedAlignmentPlusVector.h
+@@ -15,6 +15,7 @@
+ 
+ #include "Alignment.h"
+ 
+using std::streampos;
+ 
+ // This class encapsulates the header information for both vectors and indices.
+ 
+--- vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc
+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc
+@@ -10,6 +10,7 @@
+ #include "kmers/KmerParcels.h"
+ #include "system/WorklistN.h"
+ 
+using std::fixed;
+ 
+ inline String Tag(String S = "KPs") { return Date() + " (" + S + "): "; } 
+ 
+--- vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h
+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h
+@@ -6,6 +6,9 @@
+ //   Institute is not responsible for its use, misuse, or functionality.     //
+ ///////////////////////////////////////////////////////////////////////////////
+ 
+using std::hex;
+using std::dec;
+
+ // ---------------------------------
+ // NaifTimer
+ // ---------------------------------
+--- vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h
+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h
+@@ -10,7 +10,7 @@
+ #ifndef KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H
+ #define KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H
+ 
+-
+using std::map;
+ 
+ // --------------------------------------
+ // MapOfCounters
+--- vaal-46233/src/layout/ContigActualloc.h
+++ vaal-46233/src/layout/ContigActualloc.h
+@@ -17,6 +17,8 @@
+ #include "system/Crash.h"
+ #include "Misc.h"
+ 
+using std::set;
+using std::map;
+ 
+ //
+ // Class contig_actualloc
+--- vaal-46233/src/lookup/ImperfectLookup.h
+++ vaal-46233/src/lookup/ImperfectLookup.h
+@@ -52,6 +52,8 @@
+ #include "lookup/AlignCollector.h"
+ #include "solid/Solid.h"
+ 
+using std::unique_ptr;
+
+ class TaskTimer;
+ 
+ 
+@@ -534,7 +536,7 @@
+       aligns.resize( nqueries );
+     }
+ 
+-    auto_ptr<TaskTimer> t1, t2;
+    unique_ptr<TaskTimer> t1, t2;
+ 
+     if ( m_instr_level & IO_TIMER != 0 ) t1.reset( new TaskTimer() );
+     if ( m_instr_level & CPU_TIMER != 0 ) t2.reset( new TaskTimer() );
+--- vaal-46233/src/lookup/LookAlign.cc
+++ vaal-46233/src/lookup/LookAlign.cc
+@@ -29,6 +29,8 @@
+ #include "random/Random.h"
+ #include "system/ParsedArgs.h"
+ 
+using std::istrstream;
+
+ String QUERY("QUERY");
+ 
+ void look_align::ResetFromAlign(const align & al, const basevector & b1,
+--- vaal-46233/src/lookup/LookAlignFinder.h
+++ vaal-46233/src/lookup/LookAlignFinder.h
+@@ -12,6 +12,8 @@
+ #include "lookup/LookAlign.h"
+ #include "Vec.h"
+ 
+using std::set;
+
+ /**
+    Class: LookAlignFinder
+ 
+--- vaal-46233/src/lookup/LookAlignSort.h
+++ vaal-46233/src/lookup/LookAlignSort.h
+@@ -15,6 +15,8 @@
+ 
+ #include <functional>
+ 
+using std::set;
+
+ /// Read in look_aligns from file, sort, and load into vecs
+ /// \param fname name of look_align text file
+ /// \param aligns vector into which to put the alignments
+--- vaal-46233/src/lookup/LookupTable.h
+++ vaal-46233/src/lookup/LookupTable.h
+@@ -18,6 +18,8 @@
+ 
+ #include <set>
+ 
+using std::set;
+
+ typedef pair<unsigned int, unsigned int> LocSeq;
+ 
+ ///
+--- vaal-46233/src/lookup/QueryLookupTableCore.cc
+++ vaal-46233/src/lookup/QueryLookupTableCore.cc
+@@ -456,6 +456,9 @@
+ #include "system/ParsedArgs.h"
+ #include "system/file/FileReader.h"
+ 
+using std::istrstream;
+using std::less_equal;
+
+ #define ABORT(MSG)                                 \
+ {    out << MSG << "  Abort." << endl << endl;     \
+      exit(1);    }
+--- vaal-46233/src/lookup/ShortQueryLookup.cc
+++ vaal-46233/src/lookup/ShortQueryLookup.cc
+@@ -32,6 +32,8 @@
+ #include "lookup/AlignCollector.h"
+ #include "lookup/ImperfectLookup.h"
+ 
+using std::ios_base;
+
+ // Run an alignment processing chain: seqs -> look -> receiver -> aligns
+ // That is, look turns seqs into hits, which receiver accepts
+ // and turns into alignments which are passed to aligns.  The
+--- vaal-46233/src/Map.h
+++ vaal-46233/src/Map.h
+@@ -21,7 +21,7 @@
+ #include <map>
+ #include <ext/hash_map>
+ using namespace __gnu_cxx;
+-
+using std::map;
+ 
+ ///Return true if k is a key in map m
+ template<class Key, class Value, typename Cmp> 
+--- vaal-46233/src/math/Array.h
+++ vaal-46233/src/math/Array.h
+@@ -12,6 +12,9 @@
+ #include "CoreTools.h"
+ #include "Vec.h"
+ 
+using std::map;
+using std::fill;
+
+ // ==============================================================================
+ // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> >
+ // The elements are uninitialized.
+--- vaal-46233/src/math/Functions.cc
+++ vaal-46233/src/math/Functions.cc
+@@ -10,8 +10,8 @@
+ #include "STLExtensions.h"
+ #include "math/Functions.h"
+ 
+-
+-
+using std::isfinite;
+using std::make_pair;
+ 
+ /*  CombineNormalDistribution              Filipe Ribeiro 2009-06-22
+  *
+--- vaal-46233/src/math/Functions.h
+++ vaal-46233/src/math/Functions.h
+@@ -14,6 +14,10 @@
+ #include <cmath>
+ #include <numeric>
+ 
+using std::min;
+using std::cerr;
+using std::swap;
+
+ // ===========================================================================
+ //
+ // Min functions
+--- vaal-46233/src/math/HoInterval.cc
+++ vaal-46233/src/math/HoInterval.cc
+@@ -10,6 +10,8 @@
+ #include "math/HoInterval.h"
+ #include "STLExtensions.h"
+ 
+using std::make_pair;
+
+ bool ho_interval::Merge(const ho_interval & o) {
+   if (!Meets(*this,o)) return false;
+   *this = Span(*this, o);
+--- vaal-46233/src/math/HoInterval.h
+++ vaal-46233/src/math/HoInterval.h
+@@ -14,6 +14,8 @@
+ #include "feudal/MasterVec.h"
+ #include "feudal/SerfVec.h"
+ 
+using std::max;
+
+ /// Class: ho_interval
+ /// A half-open interval [a, b).
+ class ho_interval {
+--- vaal-46233/src/PackAlign.h
+++ vaal-46233/src/PackAlign.h
+@@ -133,6 +133,8 @@
+ #include "pairwise_aligners/Mutmer.h"
+ #include "feudal/BinaryStream.h"
+ 
+using std::make_pair;
+
+ const int Bits2  = 3, Bits3  = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, 
+   Bits16 = 65535;
+ 
+--- vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc
+++ vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc
+@@ -19,6 +19,9 @@
+ #include "pairwise_aligners/AlignFromMutmers.h"
+ #include "pairwise_aligners/SmithWatBandedA.h"
+ 
+using std::map;
+using std::set;
+
+ // If there's a perfect match of length at least perf but we produced no proper 
+ // alignment, use banded Smith-Waterman to create one.
+ 
+--- vaal-46233/src/pairwise_aligners/MatchList.cc
+++ vaal-46233/src/pairwise_aligners/MatchList.cc
+@@ -9,6 +9,8 @@
+ 
+ #include "pairwise_aligners/MatchList.h"
+ 
+using std::max;
+
+ bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const 
+ {
+   const vec<Match>& sortedMatches = m_sortedMatches[id1];
+--- vaal-46233/src/pairwise_aligners/SuffixTree.h
+++ vaal-46233/src/pairwise_aligners/SuffixTree.h
+@@ -23,6 +23,8 @@
+ #include <list>
+ #include <string>
+ 
+using std::list;
+
+ /**
+  * Implementation of a suffix tree for basevectors.
+  * This is a data structure for exact (sub)string matching.
+--- vaal-46233/src/paths/AlignHyperKmerPath.cc
+++ vaal-46233/src/paths/AlignHyperKmerPath.cc
+@@ -23,6 +23,9 @@
+ #include "paths/KmerBaseBroker.h"
+ #include "paths/KmerPath.h"
+ 
+using std::ostringstream;
+using std::set;
+
+ // Function: AlignHyperKmerPath
+ //
+ // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed
+--- vaal-46233/src/paths/AlignSeqsToHyper.cc
+++ vaal-46233/src/paths/AlignSeqsToHyper.cc
+@@ -26,6 +26,7 @@
+ #include "paths/ReadsToPathsCoreX.h"
+ #include "paths/SeqOnHyper.h"
+ 
+using std::multimap;
+ 
+ // Local class: simple_align
+ //
+--- vaal-46233/src/paths/HyperKmerPath.cc
+++ vaal-46233/src/paths/HyperKmerPath.cc
+@@ -19,6 +19,8 @@
+ #include "paths/HyperKmerPath.h"
+ #include "paths/KmerBaseBroker.h"
+ 
+using std::ostrstream;
+using std::ends;
+ 
+ void HyperKmerPath::ReduceLoops( )
+ {    for ( int v = 0; v < N( ); v++ )
+--- vaal-46233/src/paths/KmerBaseBroker.h
+++ vaal-46233/src/paths/KmerBaseBroker.h
+@@ -20,6 +20,8 @@
+ #include <algorithm>  // for set_union
+ #include <map>
+ 
+using std::map;
+
+ /**
+    Class: KmerBaseBrokerTemplate
+ 
+--- vaal-46233/src/paths/KmerPath.h
+++ vaal-46233/src/paths/KmerPath.h
+@@ -22,6 +22,8 @@
+ #include "HashSimple.h"
+ #include "graph/Digraph.h"
+ 
+using std::make_pair;
+
+ class KmerPathLoc;  // forward declaration
+ 
+ /**
+--- vaal-46233/src/paths/KmerPathInterval.h
+++ vaal-46233/src/paths/KmerPathInterval.h
+@@ -8,6 +8,8 @@
+ #include "CommonSemanticTypes.h"
+ #include "feudal/BinaryStreamTraits.h"
+ 
+using std::max;
+
+ // Portability note: endianness
+ // The implementations here would need to be changed for big endian architectures.
+ 
+@@ -285,6 +287,12 @@
+    Models <tagged read path interval>.
+ */
+ // TODO: potentially dangerous truncation of index by PathId, ReadId
+template<class TAG>
+void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 );
+
+template<class TAG>
+void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 );
+
+ class tagged_rpint {
+ 
+      public: /* PUBLIC METHODS */
+@@ -362,11 +370,11 @@
+ 
+      template<class TAG>
+      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
+-          vec<longlong>& answer, bool append = false, int cap = -1 );
+          vec<longlong>& answer, bool append, int cap );
+ 
+      template<class TAG>
+      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
+-          vec<longlong>& answer, bool append = false, int cap = -1 );
+          vec<longlong>& answer, bool append, int cap );
+ 
+      template<class TAG>
+      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
+@@ -489,11 +497,11 @@
+ 
+      template<class TAG>
+      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
+-          vec<longlong>& answer, bool append = false, int cap = -1 );
+          vec<longlong>& answer, bool append, int cap );
+ 
+      template<class TAG>
+      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
+-          vec<longlong>& answer, bool append = false, int cap = -1 );
+          vec<longlong>& answer, bool append, int cap );
+ 
+      template<class TAG>
+      friend longlong Instance( const vec<TAG>& segs, kmer_id_t k );
+@@ -620,11 +628,11 @@
+ 
+      template<class TAG>
+      friend void Contains( const vec<TAG>& segs, kmer_id_t index,
+-          vec<longlong>& answer, bool append = false, int cap = -1 );
+          vec<longlong>& answer, bool append, int cap );
+ 
+      template<class TAG>
+      friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi,
+-          vec<longlong>& answer, bool append = false, int cap = -1 );
+          vec<longlong>& answer, bool append, int cap );
+ 
+      template<class TAG>
+      friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k );
+--- vaal-46233/src/paths/ReadsToPathsCoreX.cc
+++ vaal-46233/src/paths/ReadsToPathsCoreX.cc
+@@ -20,6 +20,8 @@
+ #include "paths/MakeAlignsPathsParallelX.h"
+ #include "paths/ReadsToPathsCoreX.h"
+ 
+using std::map;
+
+ static inline 
+ String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } 
+ 
+--- vaal-46233/src/paths/SuperBaseVector.h
+++ vaal-46233/src/paths/SuperBaseVector.h
+@@ -10,6 +10,8 @@
+ #include <numeric>
+ #include <functional>
+ 
+using std::mem_fun_ref;
+
+ /// A simple class which holds a series of basevectors with
+ /// (possibly negative) gaps between them.  This is what a 
+ /// KmerPath logically maps to in sequence space.  The function
+--- vaal-46233/src/polymorphism/VAAL2.cc
+++ vaal-46233/src/polymorphism/VAAL2.cc
+@@ -42,7 +42,7 @@
+ #include "feudal/BinaryStream.h"
+ #include "feudal/VirtualMasterVec.h"
+ 
+-using namespace std;
+
+ 
+ // Trim reads so that they contain only kmers in the unipaths.
+ 
+--- vaal-46233/src/polymorphism/VAAL3.cc
+++ vaal-46233/src/polymorphism/VAAL3.cc
+@@ -29,6 +29,8 @@
+ #include "polymorphism/VAALTools.h"
+ #include "solexa/SolexaTools.h"
+ 
+using std::ostringstream;
+
+ int main( int argc, char *argv[] )
+ {
+      RunTime( );
+--- vaal-46233/src/PrintAlignment.h
+++ vaal-46233/src/PrintAlignment.h
+@@ -14,6 +14,8 @@
+ #include "CoreTools.h"
+ #include "Qualvector.h"
+ 
+using std::ostringstream;
+
+ void PrintBlanks( ostream& out, int n );
+ 
+ template<class BASEVEC>
+--- vaal-46233/src/Qualvector.cc
+++ vaal-46233/src/Qualvector.cc
+@@ -10,6 +10,8 @@
+ #include "FastIfstream.h"
+ #include "Qualvector.h"
+ 
+using std::istrstream;
+
+ /// \file
+ /// \ingroup grp_quals
+ /// \copydoc Qualvector.h
+--- vaal-46233/src/SeqInterval.cc
+++ vaal-46233/src/SeqInterval.cc
+@@ -9,6 +9,8 @@
+ #include "SeqInterval.h"
+ #include "Vec.h"
+ 
+using std::max;
+using std::min;
+ 
+ /*
+  * seq_interval
+--- vaal-46233/src/SeqInterval.h
+++ vaal-46233/src/SeqInterval.h
+@@ -14,7 +14,9 @@
+ #include <algorithm>
+ #include <iostream>
+ 
+-using namespace std;
+using std::binary_function;
+using std::ostream;
+using std::istream;
+ 
+ /*
+  * class seq_interval
+--- vaal-46233/src/Set.h
+++ vaal-46233/src/Set.h
+@@ -16,7 +16,7 @@
+ #include <set>
+ #include "CoreTools.h"
+ 
+-using namespace std;
+using std::set;
+ 
+ template<class T> bool Member( const set<T>& the_set, const T& value )
+ {    return the_set.find(value) != the_set.end( );    }  // Breaks cxx 
+--- vaal-46233/src/ShortVector.h
+++ vaal-46233/src/ShortVector.h
+@@ -14,6 +14,8 @@
+ #include "system/Types.h"
+ #include "feudal/BinaryStream.h"
+ 
+using std::uninitialized_fill_n;
+
+ // ================================================================================
+ //
+ // A shortvector holds a list of up to 255 things of any type T.  
+--- vaal-46233/src/solexa/FourBase2.h
+++ vaal-46233/src/solexa/FourBase2.h
+@@ -15,6 +15,10 @@
+ #include "feudal/MasterVec.h"
+ #include "feudal/SerfVec.h"
+ 
+using std::max_element;
+using std::min_element;
+using std::accumulate;
+
+ class four_base2 {
+ 
+ public:
+--- vaal-46233/src/solexa/FourBase.cc
+++ vaal-46233/src/solexa/FourBase.cc
+@@ -9,6 +9,9 @@
+ 
+ #include "solexa/FourBase.h"
+ 
+using std::string;
+using std::istringstream;
+
+ int four_base::Call( ) const
+ {
+     int result = 0;
+--- vaal-46233/src/solexa/FourBase.h
+++ vaal-46233/src/solexa/FourBase.h
+@@ -16,6 +16,8 @@
+ #include "feudal/MasterVec.h"
+ #include "feudal/SerfVec.h"
+ 
+using std::max;
+
+ /*
+    Class: four_base
+ 
+--- vaal-46233/src/solexa/SolexaMetrics.h
+++ vaal-46233/src/solexa/SolexaMetrics.h
+@@ -42,6 +42,8 @@
+ #include "CommonSemanticTypes.h"
+ #include <map>
+ 
+using std::map;
+
+ /// Definition of general macros.
+ 
+ class solexa_metric_db {
+--- vaal-46233/src/solexa/SolexaTools.cc
+++ vaal-46233/src/solexa/SolexaTools.cc
+@@ -20,6 +20,8 @@
+ #include "FastaFileset.h"
+ #include "util/BaitMap.h"
+ 
+using std::ostringstream;
+
+ void SolexaPredictorParameters::SetFromFile(const String & fname) {
+   Ifstream(is, fname);
+   String params = Slurp(is);
+--- vaal-46233/src/STLExtensions.h
+++ vaal-46233/src/STLExtensions.h
+@@ -9,7 +9,7 @@
+ #ifndef STLEXTENSIONS_H
+ #define STLEXTENSIONS_H
+ 
+-using namespace std;
+
+ 
+ #include <functional>
+ #include <vector>
+@@ -21,6 +21,13 @@
+ #include "feudal/BinaryStream.h"
+ #include "system/StaticAssert.h"
+ 
+using std::binary_function;
+using std::unary_function;
+using std::pair;
+using std::bitset;
+using std::vector;
+using std::ostream;
+
+ /// minimum<T> is a function object.  
+ ///
+ /// If f is an object of class minimum<T> and x and y are objects of
+--- vaal-46233/src/system/ParsedArgs.cc
+++ vaal-46233/src/system/ParsedArgs.cc
+@@ -26,6 +26,9 @@
+ #include "system/HostName.h"
+ #include "system/UseGDB.h"
+ 
+using std::istrstream;
+using std::mem_fun_ref;
+
+ #ifndef FatalErr
+      #define FatalErr(message) { cout << message << endl << endl; exit(-1); }
+ #endif
+--- vaal-46233/src/system/ParsedArgs.h
+++ vaal-46233/src/system/ParsedArgs.h
+@@ -97,6 +97,8 @@
+ #include "TokenizeString.h"
+ #include "ParseSet.h"
+ 
+using std::stringstream;
+
+ class parsed_arg_help {
+ 
+  public:
+--- vaal-46233/src/system/ProcBuf.cc
+++ vaal-46233/src/system/ProcBuf.cc
+@@ -15,6 +15,8 @@
+ #include <sys/wait.h>
+ #include <unistd.h>
+ 
+using std::ios_base;
+
+ namespace
+ {
+ size_t const BUFFER_SIZE = 8192;
+--- vaal-46233/src/system/RunTime.cc
+++ vaal-46233/src/system/RunTime.cc
+@@ -41,6 +41,10 @@
+      #include <unwind.h>
+ #endif
+ 
+using std::strstream;
+using std::hex;
+using std::setw;
+
+ /// ===========================================================================
+ ///
+ /// ReturnAddress(i), where 0 <= i <= 100: get the return address.  The
+--- vaal-46233/src/system/RunTime.h
+++ vaal-46233/src/system/RunTime.h
+@@ -14,6 +14,8 @@
+ #include "system/Exit.h"
+ #include "system/Types.h"
+ 
+using std::ostream;
+
+ typedef void ArachneSignalHandler(int, siginfo_t*, void*);
+ 
+ void arachne_signal_handler( int signal_number, siginfo_t* info, void* context,
+--- vaal-46233/src/system/System.cc
+++ vaal-46233/src/system/System.cc
+@@ -35,6 +35,11 @@
+ 
+ #include <dirent.h>
+ 
+using std::istringstream;
+using std::istream_iterator;
+using std::ostrstream;
+using std::ends;
+
+ int SystemInternal( String command, const char *shell )
+ {
+   flush(cout);
+--- vaal-46233/src/system/System.h
+++ vaal-46233/src/system/System.h
+@@ -21,6 +21,17 @@
+ #include "system/Exit.h"
+ #include "system/file/TempFile.h"
+ 
+using std::vector;
+using std::ostream;
+using std::ofstream;
+using std::cout;
+using std::flush;
+using std::endl;
+using std::istream;
+using std::ifstream;
+using std::ios;
+using std::setprecision;
+
+ #ifndef InputErr
+      #define InputErr(message)                                               \
+      {    cout << "\nFatal error at " << Date( ) << ": " << message << endl; \
+--- vaal-46233/src/system/TraceVal.h
+++ vaal-46233/src/system/TraceVal.h
+@@ -24,6 +24,9 @@
+ #include "system/Types.h"
+ #include "system/Assert.h"
+ 
+using std::cout;
+using std::endl;
+
+ // Macros: Tracing macros
+ //   TRACEVAL_ON - undefine if you're not doing tracing
+ //   TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles
+--- vaal-46233/src/system/Types.h
+++ vaal-46233/src/system/Types.h
+@@ -14,7 +14,7 @@
+ #include <cstdlib>
+ #include <netinet/in.h>
+ 
+-using namespace std;
+
+ 
+ // This assumes that all suns run Solaris...
+ #if __sun == 1
+--- vaal-46233/src/util/BaitMap.cc
+++ vaal-46233/src/util/BaitMap.cc
+@@ -236,7 +236,7 @@
+ bool BaitMap::write(String file_name)
+ {
+     std::ofstream out(file_name.c_str());
+-    ForceAssert(out);
+    ForceAssert(static_cast<bool>(out));
+ 
+     for (unsigned int i = 0; i < this->size(); i++)
+     {
+@@ -250,7 +250,7 @@
+     }
+ 
+     out.close();
+-    ForceAssert(out);
+    ForceAssert(static_cast<bool>(out));
+ 
+     return true;
+ }
+@@ -260,7 +260,7 @@
+ bool BaitMap::write_names(String file_name)
+ {
+     std::ofstream out(file_name.c_str());
+-    ForceAssert(out);
+    ForceAssert(static_cast<bool>(out));
+ 
+     for (unsigned int i = 0; i < this->size(); i++)
+     {
+@@ -268,7 +268,7 @@
+     }
+ 
+     out.close();
+-    ForceAssert(out);
+    ForceAssert(static_cast<bool>(out));
+ 
+     return true;
+ }
+--- vaal-46233/src/util/BaitMap.h
+++ vaal-46233/src/util/BaitMap.h
+@@ -20,6 +20,8 @@
+ 
+ #include <map>
+ 
+using std::map;
+
+ class BaitMap
+ {
+ public:
+--- vaal-46233/src/util/Qualb.cc
+++ vaal-46233/src/util/Qualb.cc
+@@ -10,6 +10,8 @@
+ #include "FastIfstream.h"
+ #include "Qualvector.h"
+ 
+using std::istrstream;
+
+ int main( int argc, char *argv[] )
+ {
+      RunTime( );
+--- vaal-46233/src/Vec.h
+++ vaal-46233/src/Vec.h
+@@ -48,6 +48,14 @@
+ #include "Compare.h"
+ #include "system/file/FileReader.h"
+ 
+using std::initializer_list;
+using std::numeric_limits;
+using std::ostream_iterator;
+using std::less;
+using std::equal_to;
+using std::setfill;
+using std::setw;
+
+ /////////////////////////////////////////////////////////////////////////////
+ //
+ //  vec Class Declaration and Template Definitions
+--- vaal-46233/src/VecUtilities.h
+++ vaal-46233/src/VecUtilities.h
+@@ -37,6 +37,7 @@
+ #include "Vec.h"
+ #include <cstddef>
+ 
+using std::greater;
+ 
+ /////////////////////////////////////////////////////////////////////////////
+ //
--- a/sci-biology/vaal/vaal-46233-r1.ebuild
+++ b/sci-biology/vaal/vaal-46233-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms"
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
+SRC_URI="
+	ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
+	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
+
+LICENSE="Whitehead-MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="openmp"
+
+DEPEND=">=dev-libs/boost-1.41.0-r3"
+RDEPEND="${DEPEND}"
+
+DOCS=( "${DISTDIR}/VAAL_manual.doc" )
+PATCHES=( "${FILESDIR}/${P}_remove-namespace-std.patch" )
+
+src_prepare() {
+	sed \
+		-e '/COPYING/d' \
+		-i src/Makefile.am || die
+
+	sed \
+		-e 's:-ggdb::g' \
+		-e '/AC_OPENMP_CEHCK/d' \
+		-i configure.ac || die
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		$(use_enable openmp)
+}