superseeded by sci-biology/allpathslg

Upstream wants anybody to move over

5 files changed, 0 insertions, 699 deletions

diff --git a/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch b/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch
deleted file mode 100644
index d4fe428efa26..000000000000
--- a/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -durr work.orig/SortKmersImpl.h work/SortKmersImpl.h
---- work.orig/SortKmersImpl.h	2009-08-20 11:25:39.336695499 +0000
-+++ work/SortKmersImpl.h	2009-08-20 11:25:51.431932630 +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);
-       }
diff --git a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch b/sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch
deleted file mode 100644
index 9a90410fe95c..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch
+++ /dev/null
@@ -1,185 +0,0 @@
- MakeDepend.cc                |  9 +++++----
- Makefile.in                  | 12 ++++++------
- Makefile_g++                 |  3 ++-
- TestProgram.cc               |  1 +
- lookup/CreateLookupTab.cc    |  3 +++
- paths/AlignPairsToHyper3G.cc |  2 ++
- paths/ErrorCorrectJump.cc    |  2 ++
- reporting/FastbStats.cc      |  1 +
- util/FastaParser.cc          |  3 +++
- 9 files changed, 25 insertions(+), 11 deletions(-)
-
-diff --git a/MakeDepend.cc b/MakeDepend.cc
-index 619e6f7..b8d9c72 100644
---- a/MakeDepend.cc
-+++ b/MakeDepend.cc
-@@ -1032,7 +1032,7 @@ void makefile_builder::GenerateMakefileForSharedLibs( ostream &mf )
-       mf << " " << dep_iter->Provider();
-     mf << "\n";
-     mf << "\t" << "mkdir -p $(LIB)" << endl;
--    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) -o $(LIB)/" << *lib_iter;
-+    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) $(L_FLAGS) -o $(LIB)/" << *lib_iter;
-     for ( vector<dependency>::iterator dep_iter = link_deps.first;
-           dep_iter != link_deps.second; ++dep_iter )
-       mf << " $(OBJ)/" << dep_iter->Provider();
-@@ -1182,7 +1182,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       mf << " $(OBJ)/" << *dep_iter;     
-     }
-     mf << "\n\t$(BIN)/checkLock $(BIN)/$@";
--    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ ";
-+    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) $(L_FLAGS) -o $(BIN)/$@ ";
-     for ( set<string>::iterator dep_iter = obj_deps.begin();
-           dep_iter != obj_deps.end(); ++dep_iter )
-     {
-@@ -1195,7 +1195,8 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-         mf << " $(OBJ)/" << *dep_iter;
-       }
-     }
--    mf << " $(OBJ)/LinkTimestamp.o -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; 
-+    mf << " $(OBJ)/LinkTimestamp.o $(PTHREAD_OBJ) -L. -L$(LIB) -L$(OBJ)"; 
-+    mf << " -l" << libname;
-     for ( set<string>::iterator dep_iter = lib_deps.begin(); 
- 	  dep_iter != lib_deps.end(); ++dep_iter )
-       mf << " " << "$(" << *dep_iter << "_LFLAGS)";
-@@ -1208,7 +1209,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       sharedlib_name.erase( sharedlib_name.size() - 3, 3 );
-       mf << " -l" << sharedlib_name;
-     }
--    mf << " -l" << libname;
-+    mf << " $(LINK_LIBS)"; 
-     mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
-   }
- }    
-diff --git a/Makefile.in b/Makefile.in
-index f20db27..fe45b4c 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -106,9 +106,9 @@ vpath % $(BIN)
- ##############################################################################
- 
- # our boost dependancies
--BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- BOOST_IOSTREAMS_LFLAGS 	= -lboost_iostreams-@BOOST_TAG@
--BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- 
- # PUT OUR GMP FLAGS HERE
- GMP_LFLAGS	= @GMP_LIB@
-@@ -340,10 +340,10 @@ LINK_OPTIONS	= \
- 		$(PTHREAD_LINK)
- 
- LINK_LIBS	= \
-+		@LIBRARIES@ \
- 		@LIBS@ \
- 		$(OMP_LIBS) \
--		$(PTHREAD_LIBS) \
--		@LIBRARIES@
-+		$(PTHREAD_LIBS)
- 
- CPPO		= $(LINK_OPTIONS)
- CPPC		= $(CPP_OPTIONS) $(SYS_MEMTRACK)
-@@ -420,10 +420,10 @@ execs_size:
- MakeDepend: MakeDepend.cc
- 	@ mkdir -p $(BIN)
- 	echo $(PATH)
--	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) $(L_FLAGS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
- 
- checkLock: $(SRC)/util/checkLock.cc
--	$(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock 
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SRC)/util/checkLock.cc $(L_FLAGS) -o $(BIN)/checkLock 
- 
- MemTracker.o: MemTracker.cc
- 	@ mkdir -p $(OBJ)
-diff --git a/Makefile_g++ b/Makefile_g++
-index 8dc8572..2a29ecc 100644
---- a/Makefile_g++
-+++ b/Makefile_g++
-@@ -29,7 +29,8 @@ PIC		= -fPIC
- #############################################################
- 
- # pThread library
--PTHREAD_LFLAGS  = $(OBJ)/system/Threads.o -lpthread
-+PTHREAD_LFLAGS  = -lpthread
-+PTHREAD_OBJ	= $(OBJ)/system/Threads.o
- PTHREAD_LIB	= system/Threads.o
- 
- #### Zlib library setup ####
-diff --git a/TestProgram.cc b/TestProgram.cc
-index e779fab..b480add 100644
---- a/TestProgram.cc
-+++ b/TestProgram.cc
-@@ -1,5 +1,6 @@
- // MakeDepend: library BOOST_FILESYSTEM
- // MakeDepend: library GMPXX
-+// MakeDepend: library GMP
- #include <gmpxx.h>
- #include <iostream>
- #include <boost/filesystem/path.hpp>
-diff --git a/lookup/CreateLookupTab.cc b/lookup/CreateLookupTab.cc
-index 44f2579..ac5c3bb 100644
---- a/lookup/CreateLookupTab.cc
-+++ b/lookup/CreateLookupTab.cc
-@@ -18,6 +18,9 @@
-  * This program just builds a singly-linked list of Locations for each kmer, and then walks each
-  * list to write them out to a feudal file.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/AlignPairsToHyper3G.cc b/paths/AlignPairsToHyper3G.cc
-index 5a0fda6..7b284a8 100644
---- a/paths/AlignPairsToHyper3G.cc
-+++ b/paths/AlignPairsToHyper3G.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/ErrorCorrectJump.cc b/paths/ErrorCorrectJump.cc
-index 40c8536..bb4d779 100644
---- a/paths/ErrorCorrectJump.cc
-+++ b/paths/ErrorCorrectJump.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/reporting/FastbStats.cc b/reporting/FastbStats.cc
-index f87f295..ba7dbe3 100644
---- a/reporting/FastbStats.cc
-+++ b/reporting/FastbStats.cc
-@@ -8,6 +8,7 @@
- /////////////////////////////////////////////////////////////////////////////
- 
- // Basic stats for a fastb file.
-+// MakeDepend: library BOOST_SYSTEM
- 
- #include "Basevector.h"
- #include "math/Functions.h"
-diff --git a/util/FastaParser.cc b/util/FastaParser.cc
-index 8b3dbc8..dc1d2cf 100644
---- a/util/FastaParser.cc
-+++ b/util/FastaParser.cc
-@@ -13,6 +13,9 @@
-  *
-  * \brief Several utility classes for reading FASTA files.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
diff --git a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50.patch b/sci-biology/allpaths/files/allpaths-3.1-boost-1.50.patch
deleted file mode 100644
index 23c031041e14..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50.patch
+++ /dev/null
@@ -1,47 +0,0 @@
- configure          | 4 ++--
- system/file/File.h | 6 +++---
- 2 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/configure b/configure
-index 37b9812..b966fd7 100755
---- a/configure
-+++ b/configure
-@@ -9872,8 +9872,8 @@ $as_echo "found boost version $_version" >&6; }
-   # using system specifics
- 
-   # lets use the system library
--  BOOST_WITH_COMP="libboost_filesystem-$CC$GCC_MAJOR_MINOR-mt.a"
--  BOOST_WITHOUT="libboost_filesystem-mt.a"
-+  BOOST_WITH_COMP="libboost_filesystem-$CC$GCC_MAJOR_MINOR-mt.so"
-+  BOOST_WITHOUT="libboost_filesystem-mt.so"
- 
-   # lets say that we're checking that
-   { $as_echo "$as_me:$LINENO: checking for boost library name" >&5
-diff --git a/system/file/File.h b/system/file/File.h
-index da78272..14c9c62 100644
---- a/system/file/File.h
-+++ b/system/file/File.h
-@@ -149,7 +149,7 @@ public:
-     /// return the filename portion of the file path
-     /// e.g., /home/user/boat/file.txt would return file.txt
-     std::string Filename() const
--    { return mPath.filename(); }
-+    { return mPath.filename().string(); }
- 
-     /// return the path portion of the filename
-     /// e.g., /home/user/boat/file.txt would return /home/user/boat
-@@ -163,12 +163,12 @@ public:
-     /// return the filename with its final extension (if any) removed
-     /// e.g., /home/user/boat/file.txt would return /home/user/boat/file
-     std::string Stem() const
--    { return mPath.stem(); }
-+    { return mPath.stem().string(); }
- 
-     /// return the final extension (empty string, if there is none)
-     /// e.g., /home/user/boat/file.txt would return .txt
-     std::string Extension() const
--    { return mPath.extension(); }
-+    { return mPath.extension().string(); }
- 
-     /// make a new File with a path obtained by removing this File's final extension, if any,
-     /// and gluing on the newExtension (preceded by a '.' if it doesn't already start with one).
diff --git a/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch b/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch
deleted file mode 100644
index a2f4b4d37c75..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch
+++ /dev/null
@@ -1,264 +0,0 @@
- MakeDepend.cc                |  1 +
- Vec.h                        | 12 ++++++------
- feudal/BinaryStream.h        |  4 ++++
- feudal/FeudalControlBlock.cc |  1 +
- feudal/FeudalFileReader.h    |  1 +
- feudal/MasterVec.h           | 14 +++++++-------
- feudal/SerfVec.h             |  4 ++--
- reporting/ScaffoldLayout.cc  | 10 +++++-----
- system/ProcBuf.cc            | 12 ++++++------
- 9 files changed, 33 insertions(+), 26 deletions(-)
-
-diff --git a/MakeDepend.cc b/MakeDepend.cc
-index 93032e8..619e6f7 100644
---- a/MakeDepend.cc
-+++ b/MakeDepend.cc
-@@ -25,6 +25,7 @@
- #include <iterator>
- #include <iostream>
- #include <ctype.h>
-+#include <unistd.h>
- 
- using namespace std;
- 
-diff --git a/Vec.h b/Vec.h
-index f26f3f4..e2d26a4 100644
---- a/Vec.h
-+++ b/Vec.h
-@@ -259,11 +259,11 @@ template <class T> class vec : public vector<T> {
- 
-   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
-@@ -339,7 +339,7 @@ template <class T> class vec : public vector<T> {
-     
-   void SetToRangeOf( const vec<T>& v, size_type i, size_type j ) {
-     AssertLe( i, j );
--    assign(v.begin() + i, v.begin() + j);
-+    this->assign(v.begin() + i, v.begin() + j);
-   }
- 
-   inline friend vec<T> RangeOf( const vec<T>& v, size_type i, size_type j ) {
-@@ -397,12 +397,12 @@ template <class T> class vec : public vector<T> {
-   /// Erase: erase range of elements, where range is given by half-open interval.
- 
-   void Erase( size_type start, size_type stop ) {
--    erase( this->begin( ) + start, this->begin( ) + stop );
-+    this->erase( this->begin( ) + start, this->begin( ) + stop );
-   }
- 
-   /// EraseValue: erase all entries having the given value.
-   void EraseValue( const T& x ) {
--    erase(remove(this->begin(), this->end(), x), this->end());
-+    this->erase(remove(this->begin(), this->end(), x), this->end());
-   }
- 
-   /// print values to ostream, separated by sep.
-diff --git a/feudal/BinaryStream.h b/feudal/BinaryStream.h
-index f54d8a9..c61469b 100644
---- a/feudal/BinaryStream.h
-+++ b/feudal/BinaryStream.h
-@@ -144,6 +144,10 @@ private:
-     std::ostream& mOS;
- };
- 
-+template <typename T1, typename T2>
-+inline size_t serializedSizeof( std::pair<T1,T2>* );
-+
-+
- /// Reader of binary streams.
- class BinaryReader
- {
-diff --git a/feudal/FeudalControlBlock.cc b/feudal/FeudalControlBlock.cc
-index bc64ecd..a709320 100644
---- a/feudal/FeudalControlBlock.cc
-+++ b/feudal/FeudalControlBlock.cc
-@@ -24,6 +24,7 @@
- #include <string.h>
- #include <errno.h>
- #include <iostream>
-+#include <unistd.h>
- 
- using std::cout;
- using std::endl;
-diff --git a/feudal/FeudalFileReader.h b/feudal/FeudalFileReader.h
-index b71bf6d..073a1a1 100644
---- a/feudal/FeudalFileReader.h
-+++ b/feudal/FeudalFileReader.h
-@@ -13,6 +13,7 @@
- #include <string>
- #include <cassert>
- #include <sstream>
-+#include <unistd.h>
- #include "feudal/BinaryStream.h"
- 
- /**
-diff --git a/feudal/MasterVec.h b/feudal/MasterVec.h
-index e6477d9..b88e9fe 100644
---- a/feudal/MasterVec.h
-+++ b/feudal/MasterVec.h
-@@ -60,20 +60,20 @@ public:
-     /// 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 )
-@@ -81,7 +81,7 @@ public:
- 
-     /// 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; }
-@@ -99,7 +99,7 @@ public:
-     { if ( !append ) BaseT::clear();
-       FeudalFileReader rdr(fileName.c_str(),T::fixedDataLen());
-       size_type siz = rdr.getNElements();
--      reserve(BaseT::size()+siz);
-+      this->reserve(BaseT::size()+siz);
-       for ( size_type iii = 0; iii < siz; ++iii )
-         appendFromReader(rdr,iii);
-       return *this; }
-@@ -148,7 +148,7 @@ public:
-                            vec<int> const& entries,
-                            int /*extra*/ = 0, Bool /*pre_reserved*/ = False )
-     { VirtualMasterVec<T> vVec(fileName.c_str());
--      if ( BaseT::size() < vVec.size() ) resize(vVec.size());
-+      if ( BaseT::size() < vVec.size() ) this->resize(vVec.size());
-       vec<int>::const_iterator end(entries.end());
-       for ( vec<int>::const_iterator itr(entries.begin()); itr != end; ++itr )
-       { BaseT::operator[](*itr) = vVec[*itr]; }
-@@ -158,7 +158,7 @@ public:
-                                 size_t from, size_t to,
-                                 int /* extra */ = 0 )
-     { VirtualMasterVec<T> vVec(fileName.c_str());
--      if ( BaseT::size() < vVec.size() ) resize(vVec.size());
-+      if ( BaseT::size() < vVec.size() ) this->resize(vVec.size());
-       for ( ; from < to; ++from ) (*this)[from] = vVec[from];
-       return *this; }
- 
-diff --git a/feudal/SerfVec.h b/feudal/SerfVec.h
-index e91847c..d5f053d 100644
---- a/feudal/SerfVec.h
-+++ b/feudal/SerfVec.h
-@@ -79,10 +79,10 @@ public:
-     /// Deprecated:  Use assign().
-     SerfVec& SetToSubOf( SerfVec const& that, size_type pos, size_type len )
-     { if ( this != &that )
--      { assign(that.begin(pos),that.begin(pos+len)); }
-+      { this->assign(that.begin(pos),that.begin(pos+len)); }
-       else
-       { assert(that.size()>=pos+len);
--        erase(BaseT::begin(),BaseT::begin(pos));
-+        this->erase(BaseT::begin(),BaseT::begin(pos));
-         BaseT::resize(len); }
-       return *this; }
- 
-diff --git a/reporting/ScaffoldLayout.cc b/reporting/ScaffoldLayout.cc
-index 7c39718..646b106 100644
---- a/reporting/ScaffoldLayout.cc
-+++ b/reporting/ScaffoldLayout.cc
-@@ -66,13 +66,13 @@ int main(int argc, char **argv)
-        // This version finds the first and last non-ambiguous sequences of
-        // END_SIZE_MIN <= length <= end_size_max
-        // --bruce
--       int j, k;
-+       int l, k;
-        int end_size_max = min(END_SIZE_MAX, scaffold_size/2);
--       for (j = k = 0; k < scaffold_size; k++) {
-+       for (l = k = 0; k < scaffold_size; k++) {
- 	 if (assembly_amb[i][k]) {
--	   if (k-j >= END_SIZE_MIN) break;
--	   else j = k+1;
--	 } else if (k-j >= end_size_max) break;
-+	   if (k-l >= END_SIZE_MIN) break;
-+	   else l = k+1;
-+	 } else if (k-l >= end_size_max) break;
-        }
-        e.SetToSubOf( assembly[i], j, k-j );
-        ENDS.push_back_reserve(e);
-diff --git a/system/ProcBuf.cc b/system/ProcBuf.cc
-index 748cc6b..5b91ed3 100644
---- a/system/ProcBuf.cc
-+++ b/system/ProcBuf.cc
-@@ -189,12 +189,12 @@ basic_procbuf<charT,traits>::overflow( int_type c )
- 	    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);
-     }
-@@ -234,7 +234,7 @@ basic_procbuf<charT,traits>::pbackfail( int_type c )
- 	// (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();
-@@ -263,7 +263,7 @@ basic_procbuf<charT,traits>::flush( )
- 	// 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;
-     }
- }
-@@ -277,7 +277,7 @@ basic_procbuf<charT,traits>::fill( )
- 	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.
-@@ -312,7 +312,7 @@ basic_procbuf<charT,traits>::fill( )
-     //
-     // 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;
diff --git a/sci-biology/allpaths/files/allpaths-3.1-linking.patch b/sci-biology/allpaths/files/allpaths-3.1-linking.patch
deleted file mode 100644
index ccb54ea24530..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-linking.patch
+++ /dev/null
@@ -1,173 +0,0 @@
- MakeDepend.cc                | 9 +++++----
- Makefile.in                  | 9 +++++----
- Makefile_g++                 | 3 ++-
- TestProgram.cc               | 1 +
- lookup/CreateLookupTab.cc    | 3 +++
- paths/AlignPairsToHyper3G.cc | 2 ++
- paths/ErrorCorrectJump.cc    | 2 ++
- reporting/FastbStats.cc      | 1 +
- util/FastaParser.cc          | 3 +++
- 9 files changed, 24 insertions(+), 9 deletions(-)
-
-diff --git a/MakeDepend.cc b/MakeDepend.cc
-index 619e6f7..b8d9c72 100644
---- a/MakeDepend.cc
-+++ b/MakeDepend.cc
-@@ -1032,7 +1032,7 @@ void makefile_builder::GenerateMakefileForSharedLibs( ostream &mf )
-       mf << " " << dep_iter->Provider();
-     mf << "\n";
-     mf << "\t" << "mkdir -p $(LIB)" << endl;
--    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) -o $(LIB)/" << *lib_iter;
-+    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) $(L_FLAGS) -o $(LIB)/" << *lib_iter;
-     for ( vector<dependency>::iterator dep_iter = link_deps.first;
-           dep_iter != link_deps.second; ++dep_iter )
-       mf << " $(OBJ)/" << dep_iter->Provider();
-@@ -1182,7 +1182,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       mf << " $(OBJ)/" << *dep_iter;     
-     }
-     mf << "\n\t$(BIN)/checkLock $(BIN)/$@";
--    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ ";
-+    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) $(L_FLAGS) -o $(BIN)/$@ ";
-     for ( set<string>::iterator dep_iter = obj_deps.begin();
-           dep_iter != obj_deps.end(); ++dep_iter )
-     {
-@@ -1195,7 +1195,8 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-         mf << " $(OBJ)/" << *dep_iter;
-       }
-     }
--    mf << " $(OBJ)/LinkTimestamp.o -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; 
-+    mf << " $(OBJ)/LinkTimestamp.o $(PTHREAD_OBJ) -L. -L$(LIB) -L$(OBJ)"; 
-+    mf << " -l" << libname;
-     for ( set<string>::iterator dep_iter = lib_deps.begin(); 
- 	  dep_iter != lib_deps.end(); ++dep_iter )
-       mf << " " << "$(" << *dep_iter << "_LFLAGS)";
-@@ -1208,7 +1209,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       sharedlib_name.erase( sharedlib_name.size() - 3, 3 );
-       mf << " -l" << sharedlib_name;
-     }
--    mf << " -l" << libname;
-+    mf << " $(LINK_LIBS)"; 
-     mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
-   }
- }    
-diff --git a/Makefile.in b/Makefile.in
-index f20db27..289af1c 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -106,9 +106,10 @@ vpath % $(BIN)
- ##############################################################################
- 
- # our boost dependancies
--BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_SYSTEM = -lboost_system
-+BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- BOOST_IOSTREAMS_LFLAGS 	= -lboost_iostreams-@BOOST_TAG@
--BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- 
- # PUT OUR GMP FLAGS HERE
- GMP_LFLAGS	= @GMP_LIB@
-@@ -420,10 +421,10 @@ execs_size:
- MakeDepend: MakeDepend.cc
- 	@ mkdir -p $(BIN)
- 	echo $(PATH)
--	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) $(L_FLAGS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
- 
- checkLock: $(SRC)/util/checkLock.cc
--	$(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock 
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SRC)/util/checkLock.cc $(L_FLAGS) -o $(BIN)/checkLock 
- 
- MemTracker.o: MemTracker.cc
- 	@ mkdir -p $(OBJ)
-diff --git a/Makefile_g++ b/Makefile_g++
-index 8dc8572..2a29ecc 100644
---- a/Makefile_g++
-+++ b/Makefile_g++
-@@ -29,7 +29,8 @@ PIC		= -fPIC
- #############################################################
- 
- # pThread library
--PTHREAD_LFLAGS  = $(OBJ)/system/Threads.o -lpthread
-+PTHREAD_LFLAGS  = -lpthread
-+PTHREAD_OBJ	= $(OBJ)/system/Threads.o
- PTHREAD_LIB	= system/Threads.o
- 
- #### Zlib library setup ####
-diff --git a/TestProgram.cc b/TestProgram.cc
-index e779fab..b480add 100644
---- a/TestProgram.cc
-+++ b/TestProgram.cc
-@@ -1,5 +1,6 @@
- // MakeDepend: library BOOST_FILESYSTEM
- // MakeDepend: library GMPXX
-+// MakeDepend: library GMP
- #include <gmpxx.h>
- #include <iostream>
- #include <boost/filesystem/path.hpp>
-diff --git a/lookup/CreateLookupTab.cc b/lookup/CreateLookupTab.cc
-index 44f2579..ac5c3bb 100644
---- a/lookup/CreateLookupTab.cc
-+++ b/lookup/CreateLookupTab.cc
-@@ -18,6 +18,9 @@
-  * This program just builds a singly-linked list of Locations for each kmer, and then walks each
-  * list to write them out to a feudal file.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/AlignPairsToHyper3G.cc b/paths/AlignPairsToHyper3G.cc
-index 5a0fda6..7b284a8 100644
---- a/paths/AlignPairsToHyper3G.cc
-+++ b/paths/AlignPairsToHyper3G.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/ErrorCorrectJump.cc b/paths/ErrorCorrectJump.cc
-index 40c8536..bb4d779 100644
---- a/paths/ErrorCorrectJump.cc
-+++ b/paths/ErrorCorrectJump.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/reporting/FastbStats.cc b/reporting/FastbStats.cc
-index f87f295..ba7dbe3 100644
---- a/reporting/FastbStats.cc
-+++ b/reporting/FastbStats.cc
-@@ -8,6 +8,7 @@
- /////////////////////////////////////////////////////////////////////////////
- 
- // Basic stats for a fastb file.
-+// MakeDepend: library BOOST_SYSTEM
- 
- #include "Basevector.h"
- #include "math/Functions.h"
-diff --git a/util/FastaParser.cc b/util/FastaParser.cc
-index 8b3dbc8..dc1d2cf 100644
---- a/util/FastaParser.cc
-+++ b/util/FastaParser.cc
-@@ -13,6 +13,9 @@
-  *
-  * \brief Several utility classes for reading FASTA files.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif