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authorTed Tanberry <ted.tanberry@gmail.com>2015-12-27 13:50:04 +0100
committerTed Tanberry <ted.tanberry@gmail.com>2015-12-27 13:50:04 +0100
commite4e2a2eb17787fe55bdba387688befbaf6fb77fc (patch)
tree8ab3e6c173da2887a7472f317cf8a73fad02e57a /sci-biology
parentsci-biology/vaal: Gentoo-Bug: 568438, fix global namespace std:: clash. (diff)
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sci-biology/vaal: Remove old patches
Package-Manager: portage-2.2.26
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/vaal/files/vaal-1.2-as-needed.patch22
-rw-r--r--sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch39
-rw-r--r--sci-biology/vaal/files/vaal-1.2-respect-flags.patch60
-rw-r--r--sci-biology/vaal/files/vaal-1.6-gcc47.patch153
-rw-r--r--sci-biology/vaal/files/vaal-1.6-respect-flags.patch12
5 files changed, 0 insertions, 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 31649010dbe..00000000000
--- 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 c021fadb44b..00000000000
--- 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 d3420556b60..00000000000
--- 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 0d80f08d3c2..00000000000
--- 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@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
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 152fb423e92..00000000000
--- 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)