[med-svn] r10818 - in trunk/packages/ncbi-blast+/trunk/debian: . patches
Aaron M. Ucko
ucko at alioth.debian.org
Fri May 11 00:37:37 UTC 2012
Author: ucko
Date: 2012-05-11 00:37:37 +0000 (Fri, 11 May 2012)
New Revision: 10818
Added:
trunk/packages/ncbi-blast+/trunk/debian/patches/fix_gcc47_errors
Modified:
trunk/packages/ncbi-blast+/trunk/debian/changelog
trunk/packages/ncbi-blast+/trunk/debian/patches/series
Log:
debian/patches/fix_gcc47_errors: fix various GCC 4.7 compilation
errors and warnings. (Closes: #669679.)
* Explicitly qualify more dependent names originating in base templates.
* Directly #include headers as needed.
* Use modern syntax for making protected base members public.
* Add forward declarations as needed.
Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-05-11 00:24:23 UTC (rev 10817)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-05-11 00:37:37 UTC (rev 10818)
@@ -2,10 +2,18 @@
* NOT YET RELEASED.
- [Andreas Tille]
+ [ Aaron M. Ucko ]
+ * debian/patches/fix_gcc47_errors: fix various GCC 4.7 compilation
+ errors and warnings. (Closes: #669679.)
+ - Explicitly qualify more dependent names originating in base templates.
+ - Directly #include headers as needed.
+ - Use modern syntax for making protected base members public.
+ - Add forward declarations as needed.
+
+ [ Andreas Tille ]
* debian/control: Modernize Vcs-* fields.
- -- Aaron M. Ucko <ucko at debian.org> Thu, 10 May 2012 18:27:00 -0400
+ -- Aaron M. Ucko <ucko at debian.org> Thu, 10 May 2012 20:37:32 -0400
ncbi-blast+ (2.2.26-2) unstable; urgency=low
Added: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_gcc47_errors
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_gcc47_errors (rev 0)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_gcc47_errors 2012-05-11 00:37:37 UTC (rev 10818)
@@ -0,0 +1,320 @@
+Subject: fix various GCC 4.7 compilation errors and warnings
+
+ * Explicitly qualify more dependent names originating in base templates.
+ * Directly #include headers as needed.
+ * Use modern syntax for making protected base members public.
+ * Add forward declarations as needed.
+
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2012-04-13
+--- a/c++/include/connect/ncbi_conn_stream.hpp
++++ b/c++/include/connect/ncbi_conn_stream.hpp
+@@ -259,7 +259,7 @@
+ class CConn_IOStreamSetReadTimeout : protected CConn_IOStreamSetTimeout
+ {
+ public:
+- CConn_IOStreamSetTimeout::GetTimeout;
++ using CConn_IOStreamSetTimeout::GetTimeout;
+
+ protected:
+ CConn_IOStreamSetReadTimeout(const STimeout* timeout)
+@@ -289,7 +289,7 @@
+ class CConn_IOStreamSetWriteTimeout : protected CConn_IOStreamSetTimeout
+ {
+ public:
+- CConn_IOStreamSetTimeout::GetTimeout;
++ using CConn_IOStreamSetTimeout::GetTimeout;
+
+ protected:
+ CConn_IOStreamSetWriteTimeout(const STimeout* timeout)
+--- a/c++/include/corelib/ncbiexpt.hpp
++++ b/c++/include/corelib/ncbiexpt.hpp
+@@ -852,7 +852,7 @@
+ exception_class(const exception_class& other) \
+ : base_class(other) \
+ { \
+- x_Assign(other); \
++ this->x_Assign(other); \
+ } \
+ public: \
+ virtual ~exception_class(void) throw() {} \
+@@ -1172,7 +1172,7 @@
+ : TBase( other)
+ {
+ m_Errno = other.m_Errno;
+- x_Assign(other);
++ this->x_Assign(other);
+ }
+
+ /// Destructor.
+--- a/c++/include/corelib/ncbimisc.hpp
++++ b/c++/include/corelib/ncbimisc.hpp
+@@ -39,6 +39,7 @@
+ #ifdef HAVE_SYS_TYPES_H
+ # include <sys/types.h>
+ #endif
++#include <cstdlib>
+ #ifdef NCBI_COMPILER_ICC
+ // Preemptively pull in <cctype>, which breaks if we've already
+ // repointed is* at NCBI_is*.
+--- a/c++/include/corelib/ncbistl.hpp
++++ b/c++/include/corelib/ncbistl.hpp
+@@ -37,6 +37,7 @@
+
+ #include <common/ncbi_export.h>
+
++#include <algorithm>
+
+ // Get rid of some warnings in MSVC++
+ #if (_MSC_VER >= 1200)
+--- a/c++/include/corelib/ncbistr.hpp
++++ b/c++/include/corelib/ncbistr.hpp
+@@ -3039,7 +3039,7 @@
+ : TBase(other)
+ {
+ m_Pos = other.m_Pos;
+- x_Assign(other);
++ this->x_Assign(other);
+ }
+
+ /// Destructor.
+--- a/c++/include/serial/impl/stltypes.hpp
++++ b/c++/include/serial/impl/stltypes.hpp
+@@ -412,6 +412,7 @@
+ typedef StlIterator TStlIterator;
+ typedef TypeInfoIterator TTypeInfoIterator;
+ typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr;
++ typedef CStlClassInfoFunctions<Container> CParent;
+
+ static TStlIterator& It(TTypeInfoIterator& iter)
+ {
+@@ -437,7 +438,8 @@
+ }
+ static bool InitIterator(TTypeInfoIterator& iter)
+ {
+- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin();
++ TStlIterator stl_iter
++ = CParent::Get(iter.GetContainerPtr()).begin();
+ if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) {
+ void* data = &iter.m_IteratorData;
+ new (data) TStlIterator(stl_iter);
+@@ -445,7 +447,7 @@
+ else {
+ iter.m_IteratorData = new TStlIterator(stl_iter);
+ }
+- return stl_iter != Get(iter.GetContainerPtr()).end();
++ return stl_iter != CParent::Get(iter.GetContainerPtr()).end();
+ }
+ static void ReleaseIterator(TTypeInfoIterator& iter)
+ {
+@@ -466,7 +468,7 @@
+
+ static bool NextElement(TTypeInfoIterator& iter)
+ {
+- return ++It(iter) != Get(iter.GetContainerPtr()).end();
++ return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end();
+ }
+ static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter)
+ {
+@@ -503,7 +505,7 @@
+
+ static bool EraseElement(TTypeInfoIterator& iter)
+ {
+- TStlIterator& it = It(iter);
++ TStlIterator& it = CParent::It(iter);
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+ it = c->erase(it);
+ return it != c->end();
+@@ -511,7 +513,7 @@
+ static void EraseAllElements(TTypeInfoIterator& iter)
+ {
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+- c->erase(It(iter), c->end());
++ c->erase(CParent::It(iter), c->end());
+ }
+
+ static void SetIteratorFunctions(CStlOneArgTemplate* info)
+@@ -542,7 +544,7 @@
+ }
+ static bool EraseElement(TTypeInfoIterator& iter)
+ {
+- TStlIterator& it = It(iter);
++ TStlIterator& it = CParent::It(iter);
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+ TStlIterator erase = it++;
+ c->erase(erase);
+@@ -551,7 +553,7 @@
+ static void EraseAllElements(TTypeInfoIterator& iter)
+ {
+ Container* c = static_cast<Container*>(iter.GetContainerPtr());
+- c->erase(It(iter), c->end());
++ c->erase(CParent::It(iter), c->end());
+ }
+
+ static void SetIteratorFunctions(CStlOneArgTemplate* info)
+--- a/c++/include/serial/iterator.hpp
++++ b/c++/include/serial/iterator.hpp
+@@ -520,13 +520,13 @@
+ 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)
+--- a/c++/include/util/bitset/bmfunc.h
++++ b/c++/include/util/bitset/bmfunc.h
+@@ -39,6 +39,13 @@
+ namespace bm
+ {
+
++bm::id_t bit_block_any_range(const bm::word_t* block,
++ bm::word_t left,
++ bm::word_t right);
++
++bm::id_t bit_block_calc_count_range(const bm::word_t* block,
++ bm::word_t left,
++ bm::word_t right);
+
+ /*!
+ @brief Structure with statistical information about bitset's memory
+--- a/c++/include/util/bitset/bmserial.h
++++ b/c++/include/util/bitset/bmserial.h
+@@ -1381,7 +1381,7 @@
+ 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 @@
+ (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);
+--- a/c++/include/util/linkedset.hpp
++++ b/c++/include/util/linkedset.hpp
+@@ -268,10 +268,10 @@
+ pair<iterator, bool> ins = m_Container.insert(value);
+ if ( ins.second ) {
+ if ( ins.first == begin() )
+- insertToStart(*ins.first);
++ this->insertToStart(*ins.first);
+ else {
+ iterator prev = ins.first;
+- insertAfter(*--prev, *ins.first);
++ this->insertAfter(*--prev, *ins.first);
+ }
+ }
+ return ins;
+@@ -280,10 +280,10 @@
+ void erase(iterator iter)
+ {
+ if ( iter == begin() )
+- removeFromStart(*iter);
++ this->removeFromStart(*iter);
+ else {
+ iterator prev = iter;
+- removeAfter(*--prev, *iter);
++ this->removeAfter(*--prev, *iter);
+ }
+ m_Container.erase(iter);
+ }
+@@ -422,10 +422,10 @@
+ {
+ 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 @@
+ 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);
+ }
+--- a/c++/include/util/rangemap.hpp
++++ b/c++/include/util/rangemap.hpp
+@@ -578,7 +578,7 @@
+ // get level
+
+ // insert element
+- TSelectMapI selectIter = insertLevel(selectKey);
++ TSelectMapI selectIter = this->insertLevel(selectKey);
+ pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value);
+
+ pair<iterator, bool> ret;
+@@ -640,7 +640,7 @@
+ // 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;
+--- a/c++/src/serial/stdtypes.cpp
++++ b/c++/src/serial/stdtypes.cpp
+@@ -720,7 +720,7 @@
+ if ( IsSigned() ) {
+ // signed -> unsigned
+ // check for negative value
+- if ( IsNegative(value) )
++ if ( CParent::IsNegative(value) )
+ ThrowIntegerOverflow();
+ }
+ if ( sizeof(value) > sizeof(result) ) {
+@@ -751,7 +751,7 @@
+ // unsigned -> signed
+ if ( sizeof(value) == sizeof(result) ) {
+ // same size - check for sign change only
+- if ( IsNegative(result) )
++ if ( CParent::IsNegative(result) )
+ ThrowIntegerOverflow();
+ }
+ }
+@@ -786,7 +786,7 @@
+ if ( IsSigned() ) {
+ // signed -> unsigned
+ // check for negative value
+- if ( IsNegative(value) )
++ if ( CParent::IsNegative(value) )
+ ThrowIntegerOverflow();
+ }
+ if ( sizeof(value) > sizeof(result) ) {
+@@ -817,7 +817,7 @@
+ // unsigned -> signed
+ if ( sizeof(value) == sizeof(result) ) {
+ // same size - check for sign change only
+- if ( IsNegative(result) )
++ if ( CParent::IsNegative(result) )
+ ThrowIntegerOverflow();
+ }
+ }
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2012-05-11 00:24:23 UTC (rev 10817)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series 2012-05-11 00:37:37 UTC (rev 10818)
@@ -3,3 +3,4 @@
fix_lib_deps
no_multiarch_rpath
wrong_path_to_touch.patch
+fix_gcc47_errors
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