[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/files/

[Justin Lecher]

commit:     e4e2a2eb17787fe55bdba387688befbaf6fb77fc
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sun Dec 27 12:50:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 27 12:50:04 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4e2a2eb

sci-biology/vaal: Remove old patches

Package-Manager: portage-2.2.26

 sci-biology/vaal/files/vaal-1.2-as-needed.patch    |  22 ---
 .../vaal/files/vaal-1.2-gcc-x86-no-autocast.patch  |  39 ------
 .../vaal/files/vaal-1.2-respect-flags.patch        |  60 --------
 sci-biology/vaal/files/vaal-1.6-gcc47.patch        | 153 ---------------------
 .../vaal/files/vaal-1.6-respect-flags.patch        |  12 --
 5 files changed, 286 deletions(-)

diff --git a/sci-biology/vaal/files/vaal-1.2-as-needed.patch b/sci-biology/vaal/files/vaal-1.2-as-needed.patch
deleted file mode 100644
index 3164901..0000000
--- a/sci-biology/vaal/files/vaal-1.2-as-needed.patch
+++ /dev/null
@@ -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";
-   }
- }    

diff --git 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
deleted file mode 100644
index c021fad..0000000
--- a/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch
+++ /dev/null
@@ -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);
- 	  }

diff --git a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
deleted file mode 100644
index d342055..0000000
--- a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch
+++ /dev/null
@@ -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

diff --git a/sci-biology/vaal/files/vaal-1.6-gcc47.patch b/sci-biology/vaal/files/vaal-1.6-gcc47.patch
deleted file mode 100644
index 0d80f08..0000000
--- a/sci-biology/vaal/files/vaal-1.6-gcc47.patch
+++ /dev/null
@@ -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@g.o>
---- 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

diff --git a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
deleted file mode 100644
index 152fb42..0000000
--- a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
+++ /dev/null
@@ -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)