diff options
author | Justin Lecher <jlec@gentoo.org> | 2012-06-03 12:53:18 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2012-06-03 12:53:18 +0000 |
commit | 5d1391bb60fe9ea662fa745d505fbd116d3f459d (patch) | |
tree | d999047ee02e29cececd49817fa1f96e96d9a851 /sci-biology/ncbi-tools++ | |
parent | Add fix for underlinking detected by gold; correct eclass inherits following ... (diff) | |
download | gentoo-2-5d1391bb60fe9ea662fa745d505fbd116d3f459d.tar.gz gentoo-2-5d1391bb60fe9ea662fa745d505fbd116d3f459d.tar.bz2 gentoo-2-5d1391bb60fe9ea662fa745d505fbd116d3f459d.zip |
sci-biology/ncbi-tools++: Fix for gcc-4.7; add rpath on prefix
(Portage version: 2.2.0_alpha109/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology/ncbi-tools++')
-rw-r--r-- | sci-biology/ncbi-tools++/ChangeLog | 9 | ||||
-rw-r--r-- | sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch | 643 | ||||
-rw-r--r-- | sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild | 7 |
3 files changed, 655 insertions, 4 deletions
diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index b00919e4ef5f..050b47a5695c 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/ncbi-tools++ -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.22 2011/11/24 09:12:21 jlec Exp $ +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.23 2012/06/03 12:53:18 jlec Exp $ + + 03 Jun 2012; Justin Lecher <jlec@gentoo.org> + ncbi-tools++-2010.06.15-r1.ebuild, + +files/ncbi-tools++-2010.06.15-gcc47.patch: + Fix for gcc-4.7; add rpath on prefix 24 Nov 2011; Justin Lecher <jlec@gentoo.org> ncbi-tools++-2010.06.15-r1.ebuild, diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch new file mode 100644 index 000000000000..36718d161ac0 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-2010.06.15-gcc47.patch @@ -0,0 +1,643 @@ + include/algo/gnomon/gnomon_model.hpp | 8 +- + include/corelib/ncbiexpt.hpp | 4 +- + include/corelib/ncbimisc.hpp | 2 + + include/corelib/ncbiobj.hpp | 2 +- + include/corelib/ncbistl.hpp | 2 +- + include/corelib/ncbistr.hpp | 2 +- + include/serial/impl/stltypes.hpp | 14 +- + include/serial/iterator.hpp | 6 +- + include/util/bitset/bmfunc.h | 263 +++++++++++++------------ + include/util/bitset/bmserial.h | 6 +- + include/util/linkedset.hpp | 8 +- + include/util/rangemap.hpp | 2 +- + src/algo/blast/gumbel_params/njn_approx.hpp | 1 + + src/algo/blast/gumbel_params/sls_alp_data.hpp | 1 + + src/serial/stdtypes.cpp | 8 +- + 15 files changed, 167 insertions(+), 162 deletions(-) + +diff --git a/include/algo/gnomon/gnomon_model.hpp b/include/algo/gnomon/gnomon_model.hpp +index 66e7765..ca4d765 100644 +--- a/include/algo/gnomon/gnomon_model.hpp ++++ b/include/algo/gnomon/gnomon_model.hpp +@@ -627,11 +627,11 @@ public: + CModelCluster(TSignedSeqRange limits) : m_limits(limits) {} + void Insert(const Model& a) { + m_limits.CombineWith(a.Limits()); +- push_back(a); ++ this->push_back(a); + } + void Splice(CModelCluster& c) { // elements removed from c and inserted into *this + m_limits.CombineWith(c.Limits()); +- splice(list<Model>::end(),c); ++ this->splice(list<Model>::end(),c); + } + TSignedSeqRange Limits() const { return m_limits; } + bool operator<(const CModelCluster& c) const { return Precede(m_limits, c.m_limits); } +@@ -663,9 +663,9 @@ class NCBI_XALGOGNOMON_EXPORT CModelClusterSet : public set<Cluster> { + pair<Titerator,Titerator> lim = set<Cluster>::equal_range(clust); + for(Titerator it = lim.first; it != lim.second;) { + clust.Splice(const_cast<Cluster&>(*it)); +- erase(it++); ++ this->erase(it++); + } +- const_cast<Cluster&>(*insert(lim.second,Cluster(clust.Limits()))).Splice(clust); ++ const_cast<Cluster&>(*this->insert(lim.second,Cluster(clust.Limits()))).Splice(clust); + } + }; + +diff --git a/include/corelib/ncbiexpt.hpp b/include/corelib/ncbiexpt.hpp +index 1d3cce3..1055d66 100644 +--- a/include/corelib/ncbiexpt.hpp ++++ b/include/corelib/ncbiexpt.hpp +@@ -843,7 +843,7 @@ const TTo* UppermostCast(const TFrom& from) + exception_class(const exception_class& other) \ + : base_class(other) \ + { \ +- x_Assign(other); \ ++ this->x_Assign(other); \ + } \ + public: \ + virtual ~exception_class(void) throw() {} \ +@@ -1166,7 +1166,7 @@ public: + : TBase( other) + { + m_Errno = other.m_Errno; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +diff --git a/include/corelib/ncbimisc.hpp b/include/corelib/ncbimisc.hpp +index 87236c7..b540038 100644 +--- a/include/corelib/ncbimisc.hpp ++++ b/include/corelib/ncbimisc.hpp +@@ -47,6 +47,8 @@ + # include <ctype.h> + #endif + ++// for free() ++#include <stdlib.h> + + #if defined(_DEBUG) && !defined(NCBI_NO_STRICT_CTYPE_ARGS) + # define NCBI_STRICT_CTYPE_ARGS +diff --git a/include/corelib/ncbiobj.hpp b/include/corelib/ncbiobj.hpp +index de4c454..084a041 100644 +--- a/include/corelib/ncbiobj.hpp ++++ b/include/corelib/ncbiobj.hpp +@@ -2128,7 +2128,7 @@ public: + CIRef<Interface, TThisType> ref( + dynamic_cast<Interface*>(proxy->GetLockedObject()), *this); + if (ref.NotNull()) { +- Unlock(ref.GetPointer()); ++ this->Unlock(ref.GetPointer()); + } + return ref; + } +diff --git a/include/corelib/ncbistl.hpp b/include/corelib/ncbistl.hpp +index afd71d2..38768c4 100644 +--- a/include/corelib/ncbistl.hpp ++++ b/include/corelib/ncbistl.hpp +@@ -36,7 +36,7 @@ + + + #include <common/ncbi_export.h> +- ++#include <string> + + // Get rid of some warnings in MSVC++ 6.00 + #if (_MSC_VER >= 1200) +diff --git a/include/corelib/ncbistr.hpp b/include/corelib/ncbistr.hpp +index e515dc6..5800223 100644 +--- a/include/corelib/ncbistr.hpp ++++ b/include/corelib/ncbistr.hpp +@@ -2439,7 +2439,7 @@ public: + : TBase(other) + { + m_Pos = other.m_Pos; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +diff --git a/include/serial/impl/stltypes.hpp b/include/serial/impl/stltypes.hpp +index abfa8b8..28254ae 100644 +--- a/include/serial/impl/stltypes.hpp ++++ b/include/serial/impl/stltypes.hpp +@@ -437,7 +437,7 @@ public: + } + static bool InitIterator(TTypeInfoIterator& iter) + { +- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin(); ++ TStlIterator stl_iter = CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).begin(); + if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) { + void* data = &iter.m_IteratorData; + new (data) TStlIterator(stl_iter); +@@ -445,7 +445,7 @@ public: + else { + iter.m_IteratorData = new TStlIterator(stl_iter); + } +- return stl_iter != Get(iter.GetContainerPtr()).end(); ++ return stl_iter != CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).end(); + } + static void ReleaseIterator(TTypeInfoIterator& iter) + { +@@ -466,7 +466,7 @@ public: + + static bool NextElement(TTypeInfoIterator& iter) + { +- return ++It(iter) != Get(iter.GetContainerPtr()).end(); ++ return ++It(iter) != CStlClassInfoFunctionsIBase::Get(iter.GetContainerPtr()).end(); + } + static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter) + { +@@ -503,7 +503,7 @@ public: + + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CStlClassInfoFunctionsI::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + it = c->erase(it); + return it != c->end(); +@@ -511,7 +511,7 @@ public: + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CStlClassInfoFunctionsI::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +@@ -542,7 +542,7 @@ public: + } + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CStlClassInfoFunctionsI_set::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + TStlIterator erase = it++; + c->erase(erase); +@@ -551,7 +551,7 @@ public: + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CStlClassInfoFunctionsI_set::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +diff --git a/include/serial/iterator.hpp b/include/serial/iterator.hpp +index eabb01b..402d7ac 100644 +--- a/include/serial/iterator.hpp ++++ b/include/serial/iterator.hpp +@@ -491,13 +491,13 @@ protected: + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo) + : m_NeedType(needType) + { +- Init(beginInfo); ++ this->Init(beginInfo); + } + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo, + const string& filter) + : m_NeedType(needType) + { +- Init(beginInfo, filter); ++ this->Init(beginInfo, filter); + } + + virtual bool CanSelect(const CConstObjectInfo& object) +@@ -599,7 +599,7 @@ public: + + CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo) + { +- Init(beginInfo); ++ this->Init(beginInfo); + return *this; + } + +diff --git a/include/util/bitset/bmfunc.h b/include/util/bitset/bmfunc.h +index bf09e2d..5489213 100644 +--- a/include/util/bitset/bmfunc.h ++++ b/include/util/bitset/bmfunc.h +@@ -1794,6 +1794,72 @@ void gap_and_to_bitset(unsigned* dest, const T* buf) + } + } + ++/*! ++ Function calculates number of 1 bits in the given array of words in ++ the range between left anf right bits (borders included) ++ Make sure the addresses are aligned. ++ ++ @ingroup bitfunc ++*/ ++inline ++bm::id_t bit_block_calc_count_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right) ++{ ++ BM_ASSERT(left <= right); ++ unsigned nword, nbit; ++ nbit = left & bm::set_word_mask; ++ const bm::word_t* word = ++ block + (nword = unsigned(left >> bm::set_word_shift)); ++ if (left == right) // special case (only 1 bit to check) ++ { ++ return (*word >> nbit) & 1; ++ } ++ bm::id_t count = 0; ++ ++ unsigned acc; ++ unsigned bitcount = right - left + 1; ++ ++ if (nbit) // starting position is not aligned ++ { ++ unsigned right_margin = nbit + (right - left); ++ ++ if (right_margin < 32) ++ { ++ unsigned mask = ++ block_set_table<true>::_right[nbit] & ++ block_set_table<true>::_left[right_margin]; ++ acc = *word & mask; ++ ++ BM_INCWORD_BITCOUNT(count, acc); ++ return count; ++ } ++ else ++ { ++ acc = *word & block_set_table<true>::_right[nbit]; ++ BM_INCWORD_BITCOUNT(count, acc); ++ bitcount -= 32 - nbit; ++ } ++ ++word; ++ } ++ ++ // now when we are word aligned, we can count bits the usual way ++ for ( ;bitcount >= 32; bitcount -= 32) ++ { ++ acc = *word++; ++ BM_INCWORD_BITCOUNT(count, acc); ++ } ++ ++ if (bitcount) // we have a tail to count ++ { ++ acc = (*word) & block_set_table<true>::_left[bitcount-1]; ++ BM_INCWORD_BITCOUNT(count, acc); ++ } ++ ++ return count; ++} ++ ++ + + /*! + \brief Compute bitcount of bit block AND masked by GAP block. +@@ -1825,6 +1891,72 @@ bm::id_t gap_bitset_and_count(const unsigned* block, const T* buf) + return count; + } + ++/*! ++ Function calculates if there is any number of 1 bits ++ in the given array of words in the range between left anf right bits ++ (borders included). Make sure the addresses are aligned. ++ ++ @ingroup bitfunc ++*/ ++inline ++bm::id_t bit_block_any_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right) ++{ ++ BM_ASSERT(left <= right); ++ ++ unsigned nbit = left; // unsigned(left & bm::set_block_mask); ++ unsigned nword = unsigned(nbit >> bm::set_word_shift); ++ nbit &= bm::set_word_mask; ++ ++ const bm::word_t* word = block + nword; ++ ++ if (left == right) // special case (only 1 bit to check) ++ { ++ return (*word >> nbit) & 1; ++ } ++ unsigned acc; ++ unsigned bitcount = right - left + 1; ++ ++ if (nbit) // starting position is not aligned ++ { ++ unsigned right_margin = nbit + (right - left); ++ if (right_margin < 32) ++ { ++ unsigned mask = ++ block_set_table<true>::_right[nbit] & ++ block_set_table<true>::_left[right_margin]; ++ acc = *word & mask; ++ return acc; ++ } ++ else ++ { ++ acc = *word & block_set_table<true>::_right[nbit]; ++ if (acc) ++ return acc; ++ bitcount -= 32 - nbit; ++ } ++ ++word; ++ } ++ ++ // now when we are word aligned, we can check bits the usual way ++ for ( ;bitcount >= 32; bitcount -= 32) ++ { ++ acc = *word++; ++ if (acc) ++ return acc; ++ } ++ ++ if (bitcount) // we have a tail to count ++ { ++ acc = (*word) & block_set_table<true>::_left[bitcount-1]; ++ if (acc) ++ return acc; ++ } ++ ++ return 0; ++} ++ + + /*! + \brief Bitcount test of bit block AND masked by GAP block. +@@ -2939,137 +3071,6 @@ bm::id_t bit_block_calc_count_change(const bm::word_t* block, + } + + +-/*! +- Function calculates number of 1 bits in the given array of words in +- the range between left anf right bits (borders included) +- Make sure the addresses are aligned. +- +- @ingroup bitfunc +-*/ +-inline +-bm::id_t bit_block_calc_count_range(const bm::word_t* block, +- bm::word_t left, +- bm::word_t right) +-{ +- BM_ASSERT(left <= right); +- unsigned nword, nbit; +- nbit = left & bm::set_word_mask; +- const bm::word_t* word = +- block + (nword = unsigned(left >> bm::set_word_shift)); +- if (left == right) // special case (only 1 bit to check) +- { +- return (*word >> nbit) & 1; +- } +- bm::id_t count = 0; +- +- unsigned acc; +- unsigned bitcount = right - left + 1; +- +- if (nbit) // starting position is not aligned +- { +- unsigned right_margin = nbit + (right - left); +- +- if (right_margin < 32) +- { +- unsigned mask = +- block_set_table<true>::_right[nbit] & +- block_set_table<true>::_left[right_margin]; +- acc = *word & mask; +- +- BM_INCWORD_BITCOUNT(count, acc); +- return count; +- } +- else +- { +- acc = *word & block_set_table<true>::_right[nbit]; +- BM_INCWORD_BITCOUNT(count, acc); +- bitcount -= 32 - nbit; +- } +- ++word; +- } +- +- // now when we are word aligned, we can count bits the usual way +- for ( ;bitcount >= 32; bitcount -= 32) +- { +- acc = *word++; +- BM_INCWORD_BITCOUNT(count, acc); +- } +- +- if (bitcount) // we have a tail to count +- { +- acc = (*word) & block_set_table<true>::_left[bitcount-1]; +- BM_INCWORD_BITCOUNT(count, acc); +- } +- +- return count; +-} +- +- +-/*! +- Function calculates if there is any number of 1 bits +- in the given array of words in the range between left anf right bits +- (borders included). Make sure the addresses are aligned. +- +- @ingroup bitfunc +-*/ +-inline +-bm::id_t bit_block_any_range(const bm::word_t* block, +- bm::word_t left, +- bm::word_t right) +-{ +- BM_ASSERT(left <= right); +- +- unsigned nbit = left; // unsigned(left & bm::set_block_mask); +- unsigned nword = unsigned(nbit >> bm::set_word_shift); +- nbit &= bm::set_word_mask; +- +- const bm::word_t* word = block + nword; +- +- if (left == right) // special case (only 1 bit to check) +- { +- return (*word >> nbit) & 1; +- } +- unsigned acc; +- unsigned bitcount = right - left + 1; +- +- if (nbit) // starting position is not aligned +- { +- unsigned right_margin = nbit + (right - left); +- if (right_margin < 32) +- { +- unsigned mask = +- block_set_table<true>::_right[nbit] & +- block_set_table<true>::_left[right_margin]; +- acc = *word & mask; +- return acc; +- } +- else +- { +- acc = *word & block_set_table<true>::_right[nbit]; +- if (acc) +- return acc; +- bitcount -= 32 - nbit; +- } +- ++word; +- } +- +- // now when we are word aligned, we can check bits the usual way +- for ( ;bitcount >= 32; bitcount -= 32) +- { +- acc = *word++; +- if (acc) +- return acc; +- } +- +- if (bitcount) // we have a tail to count +- { +- acc = (*word) & block_set_table<true>::_left[bitcount-1]; +- if (acc) +- return acc; +- } +- +- return 0; +-} + + + +diff --git a/include/util/bitset/bmserial.h b/include/util/bitset/bmserial.h +index 519cd2b..00f6c01 100644 +--- a/include/util/bitset/bmserial.h ++++ b/include/util/bitset/bmserial.h +@@ -1381,7 +1381,7 @@ deserializer<BV, DEC>::deserialize_gap(unsigned char btype, decoder_type& dec, + case set_block_arrgap: + case set_block_arrgap_egamma: + { +- unsigned arr_len = read_id_list(dec, btype, this->id_array_); ++ unsigned arr_len = this->read_id_list(dec, btype, this->id_array_); + gap_len = gap_set_array(gap_temp_block_, this->id_array_, arr_len); + break; + } +@@ -1390,7 +1390,7 @@ deserializer<BV, DEC>::deserialize_gap(unsigned char btype, decoder_type& dec, + (sizeof(gap_word_t) == 2 ? dec.get_16() : dec.get_32()); + case set_block_arrgap_egamma_inv: + case set_block_arrgap_inv: +- gap_len = read_gap_block(dec, btype, gap_temp_block_, gap_head); ++ gap_len = this->read_gap_block(dec, btype, gap_temp_block_, gap_head); + break; + default: + BM_ASSERT(0); +@@ -2763,7 +2763,7 @@ serial_stream_iterator<DEC>::get_gap_block(bm::gap_word_t* dst_block) + this->block_type_ == set_block_bit_1bit); + BM_ASSERT(dst_block); + +- read_gap_block(this->decoder_, ++ this->read_gap_block(this->decoder_, + this->block_type_, + dst_block, + this->gap_head_); +diff --git a/include/util/linkedset.hpp b/include/util/linkedset.hpp +index 0d2cba1..1d09a28 100644 +--- a/include/util/linkedset.hpp ++++ b/include/util/linkedset.hpp +@@ -422,10 +422,10 @@ public: + { + iterator iter = m_Container.insert(value); + if ( iter == begin() ) +- insertToStart(get(iter)); ++ this->insertToStart(get(iter)); + else { + iterator prev = iter; +- insertAfter(get(--prev), get(iter)); ++ this->insertAfter(get(--prev), get(iter)); + } + return iter; + } +@@ -433,10 +433,10 @@ public: + void erase(iterator iter) + { + if ( iter == begin() ) +- removeFromStart(get(iter)); ++ this->removeFromStart(get(iter)); + else { + iterator prev = iter; +- removeAfter(get(--prev), get(iter)); ++ this->removeAfter(get(--prev), get(iter)); + } + m_Container.erase(iter); + } +diff --git a/include/util/rangemap.hpp b/include/util/rangemap.hpp +index 22cf3dd..b30b39d 100644 +--- a/include/util/rangemap.hpp ++++ b/include/util/rangemap.hpp +@@ -640,7 +640,7 @@ public: + // insert element + iterator ret; + ret.m_Range = range_type::GetWhole(); +- ret.m_SelectIter = insertLevel(selectKey); ++ ret.m_SelectIter = this->insertLevel(selectKey); + ret.m_SelectIterEnd = this->m_SelectMap.end(); + ret.m_LevelIter = ret.m_SelectIter->second.insert(value); + return ret; +diff --git a/src/algo/blast/gumbel_params/njn_approx.hpp b/src/algo/blast/gumbel_params/njn_approx.hpp +index a79da93..5909cdf 100644 +--- a/src/algo/blast/gumbel_params/njn_approx.hpp ++++ b/src/algo/blast/gumbel_params/njn_approx.hpp +@@ -38,6 +38,7 @@ Contents: + + #include <corelib/ncbistl.hpp> + #include <float.h> ++#include <math.h> + + BEGIN_NCBI_SCOPE + BEGIN_SCOPE(blast) +diff --git a/src/algo/blast/gumbel_params/sls_alp_data.hpp b/src/algo/blast/gumbel_params/sls_alp_data.hpp +index 5cee936..9ff4a4c 100644 +--- a/src/algo/blast/gumbel_params/sls_alp_data.hpp ++++ b/src/algo/blast/gumbel_params/sls_alp_data.hpp +@@ -44,6 +44,7 @@ Contents: Contains input data + #include <float.h> + #include <ctime> + #include <stdlib.h> ++#include <math.h> + #include <limits> + + #ifndef NCBI_OS_MSWIN +diff --git a/src/serial/stdtypes.cpp b/src/serial/stdtypes.cpp +index 6eb0ac3..cdf5356 100644 +--- a/src/serial/stdtypes.cpp ++++ b/src/serial/stdtypes.cpp +@@ -720,7 +720,7 @@ public: + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -751,7 +751,7 @@ public: + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } +@@ -786,7 +786,7 @@ public: + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -817,7 +817,7 @@ public: + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CPrimitiveTypeInfoIntFunctions::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild index 3c395d397c4a..92a083e4dd8b 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2012 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild,v 1.4 2011/11/24 09:12:21 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2010.06.15-r1.ebuild,v 1.5 2012/06/03 12:53:18 jlec Exp $ EAPI="3" @@ -36,9 +36,12 @@ src_prepare() { src/build-system/configure || die epatch \ "${FILESDIR}"/${P}-gcc46.patch \ + "${FILESDIR}"/${P}-gcc47.patch \ "${WORKDIR}"/${P}-asneeded.patch \ "${FILESDIR}"/${P}-libpng15.patch \ "${FILESDIR}"/${P}-glibc-214.patch + + use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" } src_configure() { |