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authorMichał Górny <mgorny@gentoo.org>2017-12-10 00:22:44 +0100
committerMichał Górny <mgorny@gentoo.org>2017-12-10 01:05:29 +0100
commit930e41812a61debf91ffa4ccd81853567464962c (patch)
treea8edc641464050612f8d4317f297c2ccf614b54e /sci-biology
parentgames-arcade/*: Update Manifest hashes (diff)
downloadgentoo-930e41812a61debf91ffa4ccd81853567464962c.tar.gz
gentoo-930e41812a61debf91ffa4ccd81853567464962c.tar.bz2
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sci-biology/rmblast: [QA] Move patch to a distfile
Closes: https://bugs.gentoo.org/620616
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/rmblast/Manifest3
-rw-r--r--sci-biology/rmblast/files/rmblast-1.2-gcc47.patch865
-rw-r--r--sci-biology/rmblast/rmblast-1.2-r1.ebuild7
3 files changed, 6 insertions, 869 deletions
diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest
index 00c455fce32..383d30fdb02 100644
--- a/sci-biology/rmblast/Manifest
+++ b/sci-biology/rmblast/Manifest
@@ -1 +1,2 @@
-DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 SHA256 996be9886189364fff8ed39d4668122b2e5b8b010be47d929602416d95628eef SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 WHIRLPOOL aa3ada4297812a97614b0fe218de65d7474edfb5910e156eb09b625d45338a97b35f46876f5edf6105ead8b321a28f55ed7de2ad251bbc48ffd0cfa65ee2ac7a
+DIST rmblast-1.2-gcc47.patch.bz2 7803 BLAKE2B cd3bb1aa2b6eb9e188f28589d42ce91f027866d91013f2a6123ee61e7ce28f980b858e775bc15313cf1573f0bc827f9e663d46c1bd0d2fe218745cfbbc3781a1 SHA512 4cd72dd5c777ad866b9cf674384872de5424404b524ac536e58ab412b98b6601aa5f609d05ea2329b77f16e7aca215bbc6eb3531652e5fe81e48cf997b56d13b
+DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 BLAKE2B 6539ec8fcd345bcc1c3ecede6acec233cdc343c3df18748e195dc525f4a65fefeee8398471a26dc671bfed8612e010c26b7a8a66a3c7198f142c2e068ff72751 SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6
diff --git a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
deleted file mode 100644
index 70200d59ea4..00000000000
--- a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch
+++ /dev/null
@@ -1,865 +0,0 @@
- c++/include/corelib/ncbiexpt.hpp | 4 +-
- c++/include/corelib/ncbimisc.hpp | 2 +
- c++/include/corelib/ncbiobj.hpp | 2 +-
- c++/include/corelib/ncbistl.hpp | 6 +-
- c++/include/corelib/ncbistr.hpp | 2 +-
- c++/include/corelib/test_boost.hpp | 44 +++++-
- c++/include/dbapi/driver/dbapi_object_convert.hpp | 8 +-
- .../dbapi/driver/impl/dbapi_driver_utils.hpp | 2 +-
- c++/include/serial/impl/stltypes.hpp | 16 ++-
- c++/include/serial/iterator.hpp | 6 +-
- c++/include/serial/serialbase.hpp | 8 +-
- c++/include/util/bitset/bmfunc.h | 7 +
- c++/include/util/linkedset.hpp | 16 +--
- c++/include/util/rangemap.hpp | 4 +-
- c++/src/connect/ncbi_gnutls.c | 19 ++-
- c++/src/corelib/ncbifile.cpp | 2 +-
- c++/src/corelib/test_boost.cpp | 156 ++++++++++++++++++++-
- c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 2 +-
- c++/src/serial/stdtypes.cpp | 8 +-
- 19 files changed, 269 insertions(+), 45 deletions(-)
-
-diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp
-index a9cf850..6d90e74 100644
---- a/c++/include/corelib/ncbiexpt.hpp
-+++ b/c++/include/corelib/ncbiexpt.hpp
-@@ -831,7 +831,7 @@ 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() {} \
-@@ -1154,7 +1154,7 @@ public:
- : TBase( other)
- {
- m_Errno = other.m_Errno;
-- x_Assign(other);
-+ this->x_Assign(other);
- }
-
- /// Destructor.
-diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp
-index f45d280..f0c030d 100644
---- a/c++/include/corelib/ncbimisc.hpp
-+++ b/c++/include/corelib/ncbimisc.hpp
-@@ -57,6 +57,8 @@
- * @{
- */
-
-+#include <stdlib.h>
-+
- #ifndef NCBI_ESWITCH_DEFINED
- #define NCBI_ESWITCH_DEFINED
-
-diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp
-index 4f83db4..815c188 100644
---- a/c++/include/corelib/ncbiobj.hpp
-+++ b/c++/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/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp
-index 0bf465a..0618d9d 100644
---- a/c++/include/corelib/ncbistl.hpp
-+++ b/c++/include/corelib/ncbistl.hpp
-@@ -37,7 +37,6 @@
-
- #include <common/ncbi_export.h>
-
--
- // Get rid of some warnings in MSVC++ 6.00
- #if (_MSC_VER >= 1200)
- // too long identificator name in the debug info; truncated
-@@ -162,6 +161,9 @@ typedef int NCBI_NAME2(T_EAT_SEMICOLON_,UniqueName)
- #endif
-
- #if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_WORKSHOP)
-+# if defined(NCBI_COMPILER_GCC) && NCBI_COMPILER_VERSION >= 400
-+# include <algorithm>
-+# endif
- // This template is used by some stl algorithms (sort, reverse...)
- // We need to have our own implementation because some C++ Compiler vendors
- // implemented it by using a temporary variable and an assignment operator
-@@ -174,7 +176,7 @@ template<typename Iter>
- inline
- void iter_swap( Iter it1, Iter it2 )
- {
-- swap( *it1, * it2 );
-+ swap( *it1, *it2 );
- }
-
- END_STD_SCOPE
-diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp
-index db7054f..63e3299 100644
---- a/c++/include/corelib/ncbistr.hpp
-+++ b/c++/include/corelib/ncbistr.hpp
-@@ -2583,7 +2583,7 @@ public:
- : TBase(other)
- {
- m_Pos = other.m_Pos;
-- x_Assign(other);
-+ this->x_Assign(other);
- }
-
- /// Destructor.
-diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp
-index 69c41f3..4cd77d3 100644
---- a/c++/include/corelib/test_boost.hpp
-+++ b/c++/include/corelib/test_boost.hpp
-@@ -56,10 +56,18 @@
- # undef BOOST_AUTO_TEST_MAIN
- #endif
-
-+#ifdef NCBI_COMPILER_MSVC
-+# pragma warning(push)
-+// 'class' : class has virtual functions, but destructor is not virtual
-+# pragma warning(disable: 4265)
-+#endif
-+
-+#include <boost/version.hpp>
- #include <boost/test/auto_unit_test.hpp>
- #include <boost/test/floating_point_comparison.hpp>
- #include <boost/test/framework.hpp>
- #include <boost/test/execution_monitor.hpp>
-+#include <boost/test/parameterized_test.hpp>
-
- #include <boost/preprocessor/tuple/rem.hpp>
- #include <boost/preprocessor/repeat.hpp>
-@@ -72,6 +80,7 @@
- #undef BOOST_CHECK_THROW_IMPL
- #undef BOOST_CHECK_NO_THROW_IMPL
- #undef BOOST_FIXTURE_TEST_CASE
-+#undef BOOST_PARAM_TEST_CASE
-
- #define BOOST_CHECK_THROW_IMPL( S, E, P, prefix, TL ) \
- try { \
-@@ -109,6 +118,12 @@ catch( ... ) { \
- } \
- /**/
-
-+#if BOOST_VERSION >= 104200
-+# define NCBI_BOOST_LOCATION() , boost::execution_exception::location()
-+#else
-+# define NCBI_BOOST_LOCATION()
-+#endif
-+
- #define BOOST_FIXTURE_TEST_CASE( test_name, F ) \
- struct test_name : public F { void test_method(); }; \
- \
-@@ -124,7 +139,8 @@ static void BOOST_AUTO_TC_INVOKER( test_name )() \
- ::framework::current_test_case().p_name \
- << "\"" << ex); \
- throw boost::execution_exception( \
-- boost::execution_exception::cpp_exception_error, ""); \
-+ boost::execution_exception::cpp_exception_error, "" \
-+ NCBI_BOOST_LOCATION() ); \
- } \
- } \
- \
-@@ -142,6 +158,12 @@ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \
- void test_name::test_method() \
- /**/
-
-+#define BOOST_PARAM_TEST_CASE( function, begin, end ) \
-+ ::NCBI_NS_NCBI::NcbiTestGenTestCases( function, \
-+ BOOST_TEST_STRINGIZE( function ), \
-+ (begin), (end) ) \
-+/**/
-+
- /// Set timeout value for the test case created using auto-registration
- /// facility.
- #define BOOST_AUTO_TEST_CASE_TIMEOUT(test_name, n) \
-@@ -158,6 +180,26 @@ static struct BOOST_JOIN( test_name, _timeout_spec ) \
- } BOOST_JOIN( test_name, _timeout_spec_inst ); \
- /**/
-
-+/// Automatic registration of the set of test cases based on some function
-+/// accepting one parameter. Set of parameters used to call that function is
-+/// taken from iterator 'begin' which is incremented until it reaches 'end'.
-+///
-+/// @sa BOOST_PARAM_TEST_CASE
-+#define BOOST_AUTO_PARAM_TEST_CASE( function, begin, end ) \
-+ BOOST_AUTO_TU_REGISTRAR(function) ( \
-+ BOOST_PARAM_TEST_CASE(function, begin, end)) \
-+/**/
-+
-+#define BOOST_TIMEOUT(M) \
-+ do { \
-+ static string s(M); \
-+ throw boost::execution_exception( \
-+ boost::execution_exception::timeout_error, s \
-+ NCBI_BOOST_LOCATION()); \
-+ } while (0) \
-+/**/
-+
-+
-
- #define NCBITEST_CHECK_IMPL(P, check_descr, TL, CT) \
- BOOST_CHECK_NO_THROW_IMPL(BOOST_CHECK_IMPL(P, check_descr, TL, CT), TL)
-diff --git a/c++/include/dbapi/driver/dbapi_object_convert.hpp b/c++/include/dbapi/driver/dbapi_object_convert.hpp
-index 6fcde61..eddde81 100644
---- a/c++/include/dbapi/driver/dbapi_object_convert.hpp
-+++ b/c++/include/dbapi/driver/dbapi_object_convert.hpp
-@@ -67,7 +67,7 @@ public:
- operator const CTime&(void) const;
-
- private:
-- mutable obj_type& m_Value;
-+ obj_type& m_Value;
- };
-
- ////////////////////////////////////////////////////////////////////////////////
-@@ -92,7 +92,7 @@ public:
- operator const CTime&(void) const;
-
- private:
-- mutable obj_type& m_Value;
-+ obj_type& m_Value;
- };
-
- ////////////////////////////////////////////////////////////////////////////////
-@@ -133,7 +133,7 @@ public:
- operator const CTime&(void) const;
-
- private:
-- mutable obj_type& m_Value;
-+ obj_type& m_Value;
- };
-
- ////////////////////////////////////////////////////////////////////////////////
-@@ -174,7 +174,7 @@ public:
- operator const CTime&(void) const;
-
- private:
-- mutable obj_type& m_Value;
-+ obj_type& m_Value;
- };
-
- ////////////////////////////////////////////////////////////////////////////////
-diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-index 0792a6d..b6bd64b 100644
---- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-+++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp
-@@ -231,7 +231,7 @@ protected:
-
- private:
- const string& m_SPName;
-- mutable impl::CConnection& m_Conn;
-+ impl::CConnection& m_Conn;
- };
-
-
-diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp
-index d41ab94..7d9e3ce 100644
---- a/c++/include/serial/impl/stltypes.hpp
-+++ b/c++/include/serial/impl/stltypes.hpp
-@@ -412,6 +412,7 @@ public:
- typedef StlIterator TStlIterator;
- typedef TypeInfoIterator TTypeInfoIterator;
- typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr;
-+ typedef CStlClassInfoFunctions<Container> CParent;
-
- static TStlIterator& It(TTypeInfoIterator& iter)
- {
-@@ -437,7 +438,8 @@ public:
- }
- 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 @@ public:
- 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 @@ public:
-
- 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 @@ public:
-
- 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 @@ public:
- 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 @@ public:
- }
- 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 @@ public:
- 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)
-diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp
-index 25e1193..cddb046 100644
---- a/c++/include/serial/iterator.hpp
-+++ b/c++/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/c++/include/serial/serialbase.hpp b/c++/include/serial/serialbase.hpp
-index be6a4f9..d59fb25 100644
---- a/c++/include/serial/serialbase.hpp
-+++ b/c++/include/serial/serialbase.hpp
-@@ -364,11 +364,15 @@ public:
- // cast to object type
- TObject& operator*(void)
- {
-- return *reinterpret_cast<TObject*>(m_Buffer);
-+ TObject* ptr = static_cast<TObject*>
-+ (static_cast<void*>(m_Buffer));
-+ return *ptr;
- }
- const TObject& operator*(void) const
- {
-- return *reinterpret_cast<const TObject*>(m_Buffer);
-+ const TObject* ptr = static_cast<const TObject*>
-+ (static_cast<const void*>(m_Buffer));
-+ return *ptr;
- }
-
- // construct/destruct object
-diff --git a/c++/include/util/bitset/bmfunc.h b/c++/include/util/bitset/bmfunc.h
-index 5917ee5..a8c204b 100644
---- a/c++/include/util/bitset/bmfunc.h
-+++ b/c++/include/util/bitset/bmfunc.h
-@@ -37,6 +37,13 @@ For more information please visit: http://bmagic.sourceforge.net
- 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
-diff --git a/c++/include/util/linkedset.hpp b/c++/include/util/linkedset.hpp
-index e8bbe6e..364164b 100644
---- a/c++/include/util/linkedset.hpp
-+++ b/c++/include/util/linkedset.hpp
-@@ -268,10 +268,10 @@ public:
- 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 @@ public:
- 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 @@ 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/c++/include/util/rangemap.hpp b/c++/include/util/rangemap.hpp
-index c4f5f37..56e267d 100644
---- a/c++/include/util/rangemap.hpp
-+++ b/c++/include/util/rangemap.hpp
-@@ -578,7 +578,7 @@ public:
- // 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 @@ 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/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c
-index f0242b7..8b13713 100644
---- a/c++/src/connect/ncbi_gnutls.c
-+++ b/c++/src/connect/ncbi_gnutls.c
-@@ -98,7 +98,6 @@ static const int kGnuTlsCertPrio[] = {
- 0
- };
- static const int kGnuTlsCompPrio[] = {
-- GNUTLS_COMP_LZO,
- GNUTLS_COMP_ZLIB,
- GNUTLS_COMP_NULL,
- 0
-@@ -254,6 +253,24 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error)
- }
-
-
-+/*ARGSUSED*/
-+static void x_set_errno(gnutls_session_t session, int error)
-+{
-+# ifdef LIBGNUTLS_VERSION_NUMBER
-+# if \
-+ LIBGNUTLS_VERSION_MAJOR > 1 || \
-+ LIBGNUTLS_VERSION_MINOR > 5 || \
-+ LIBGNUTLS_VERSION_PATCH > 3
-+ gnutls_transport_set_errno(session, error);
-+ return;
-+# endif /*LIBGNUTLS_VERSION >= 1.5.4*/
-+# endif /*LIBGNUTLS_VERSION_NUMBER*/
-+ /*NOTREACHED*/
-+ if (error)
-+ errno = error;
-+}
-+
-+
- static ssize_t x_GnuTlsPull(gnutls_transport_ptr_t ptr,
- void* buf, size_t size)
- {
-diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp
-index d751e62..fdc81c7 100644
---- a/c++/src/corelib/ncbifile.cpp
-+++ b/c++/src/corelib/ncbifile.cpp
-@@ -51,8 +51,8 @@
- # include <dirent.h>
- # include <pwd.h>
- # include <fcntl.h>
--# include <sys/time.h>
- # include <sys/mman.h>
-+# include <sys/time.h>
- # ifdef HAVE_SYS_STATVFS_H
- # include <sys/statvfs.h>
- # endif
-diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp
-index dfd9cc8..f93d2ca 100644
---- a/c++/src/corelib/test_boost.cpp
-+++ b/c++/src/corelib/test_boost.cpp
-@@ -41,6 +41,7 @@
- #ifndef BOOST_TEST_NO_LIB
- # define BOOST_TEST_NO_LIB
- #endif
-+#define BOOST_TEST_NO_MAIN
- #include <corelib/test_boost.hpp>
-
- #include <boost/preprocessor/cat.hpp>
-@@ -95,6 +96,7 @@ const char* kTestResultTimeout = "timeout";
- const char* kTestResultAborted = "aborted";
- const char* kTestResultSkipped = "skipped";
- const char* kTestResultDisabled = "disabled";
-+const char* kTestResultToFix = "tofix";
-
-
- typedef but::results_reporter::format TBoostRepFormatter;
-@@ -168,14 +170,24 @@ public:
- unsigned long elapsed);
- virtual
- void test_unit_skipped(ostream& ostr, but::test_unit const& tu);
-+#if BOOST_VERSION >= 104200
-+ virtual
-+ void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd,
-+ boost::execution_exception const& ex);
-+ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
-+ using TBoostLogFormatter::log_exception;
-+#else
- virtual
- void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd,
- but::const_string explanation);
-+#endif
- virtual
- void log_entry_start (ostream& ostr, but::log_entry_data const& led,
- log_entry_types let);
- virtual
- void log_entry_value (ostream& ostr, but::const_string value);
-+ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up
-+ using TBoostLogFormatter::log_entry_value;
- virtual
- void log_entry_finish (ostream& ostr);
-
-@@ -402,10 +414,15 @@ public:
-
- /// Mark test case as failed due to hit of the timeout
- void SetTestTimedOut(but::test_case* tc);
-+ /// Register the fact of test failure
-+ void SetTestErrored(but::test_case* tc);
-+ /// Check if given test is marked as requiring fixing in the future
-+ bool IsTestToFix(const but::test_unit* tu);
-
- /// Get number of actually executed tests
- int GetRanTestsCount(void);
--
-+ /// Get number of tests that were failed but are marked to be fixed
-+ int GetToFixTestsCount(void);
- /// Get string representation of result of test execution
- string GetTestResultString(but::test_unit* tu);
-
-@@ -415,6 +432,11 @@ public:
- /// Check if user initialization functions failed
- bool IsInitFailed(void);
-
-+ /// Check if there were any test errors
-+ bool HasTestErrors(void);
-+ /// Check if there were any timeouted tests
-+ bool HasTestTimeouts(void);
-+
- private:
- typedef list<TNcbiTestUserFunction> TUserFuncsList;
-
-@@ -493,6 +515,8 @@ private:
- TUnitsSet m_DisabledTests;
- /// List of all tests which result is a timeout
- TUnitsSet m_TimedOutTests;
-+ /// List of all tests marked as in need of fixing in the future
-+ TUnitsSet m_ToFixTests;
- /// List of all dependencies for each test having dependencies
- TUnitToManyMap m_TestDeps;
- /// Observer to make test dependencies and look for unit's timeouts
-@@ -512,12 +536,18 @@ private:
- /// String representation for whole test timeout (real value taken from
- /// CHECK_TIMEOUT in Makefile).
- string m_TimeoutStr;
-+ /// Multiplicator for timeouts
-+ double m_TimeMult;
- /// Timer measuring elapsed time for the whole test
- CStopWatch m_Timer;
- /// Timeout that was set in currently executing unit before adjustment
- ///
- /// @sa AdjustTestTimeout()
- unsigned int m_CurUnitTimeout;
-+ /// Flag showing if there were some test errors
-+ bool m_HasTestErrors;
-+ /// Flag showing if there were some timeouted tests
-+ bool m_HasTestTimeouts;
- };
-
-
-@@ -794,7 +824,10 @@ CNcbiTestApplication::CNcbiTestApplication(void)
- m_RunMode (0),
- m_DummyTest(NULL),
- m_Timeout (0),
-- m_Timer (CStopWatch::eStart)
-+ m_TimeMult (1),
-+ m_Timer (CStopWatch::eStart),
-+ m_HasTestErrors(false),
-+ m_HasTestTimeouts(false)
- {
- m_Reporter = new CNcbiBoostReporter();
- m_Logger = new CNcbiBoostLogger();
-@@ -1244,6 +1277,24 @@ CNcbiTestApplication::GetRanTestsCount(void)
- return result;
- }
-
-+int
-+CNcbiTestApplication::GetToFixTestsCount(void)
-+{
-+ int result = 0;
-+ ITERATE(TUnitsSet, it, m_ToFixTests) {
-+ if (!but::results_collector.results((*it)->p_id).passed())
-+ ++result;
-+ }
-+ return result;
-+}
-+
-+inline bool
-+CNcbiTestApplication::IsTestToFix(const but::test_unit* tu)
-+{
-+ return m_ToFixTests.find(const_cast<but::test_unit*>(tu))
-+ != m_ToFixTests.end();
-+}
-+
- inline void
- CNcbiTestApplication::x_SetupBoostReporters(void)
- {
-@@ -1391,6 +1442,18 @@ CNcbiTestApplication::InitTestFramework(int argc, char* argv[])
- return NULL;
- }
-
-+inline bool
-+CNcbiTestApplication::HasTestErrors(void)
-+{
-+ return m_HasTestErrors;
-+}
-+
-+inline bool
-+CNcbiTestApplication::HasTestTimeouts(void)
-+{
-+ return m_HasTestTimeouts;
-+}
-+
- void
- CNcbiTestsCollector::visit(but::test_case const& test)
- {
-@@ -1431,9 +1494,20 @@ CNcbiTestsObserver::test_unit_finish(but::test_unit const& tu,
- // elapsed comes in microseconds
- if (timeout != 0 && timeout < elapsed / 1000000) {
- boost::execution_exception ex(
-- boost::execution_exception::timeout_error, "Timeout exceeded");
-+ boost::execution_exception::timeout_error, "Timeout exceeded"
-+ NCBI_BOOST_LOCATION());
- but::framework::exception_caught(ex);
- }
-+
-+ but::test_results& tr = but::s_rc_impl().m_results_store[tu.p_id];
-+ if (!tr.passed() && s_GetTestApp().IsTestToFix(&tu)) {
-+ static_cast<but::readwrite_property<bool>& >(
-+ static_cast<but::class_property<bool>& >(
-+ tr.p_skipped)).set(true);
-+ static_cast<but::readwrite_property<but::counter_t>& >(
-+ static_cast<but::class_property<but::counter_t>& >(
-+ tr.p_assertions_failed)).set(0);
-+ }
- }
-
- void
-@@ -1551,12 +1625,21 @@ CNcbiBoostLogger::test_unit_skipped(ostream& ostr, but::test_unit const& tu)
- m_Upper->test_unit_skipped(ostr, tu);
- }
-
-+#if BOOST_VERSION >= 104200
-+void
-+CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
-+ boost::execution_exception const& ex)
-+{
-+ m_Upper->log_exception(ostr, lcd, ex);
-+}
-+#else
- void
- CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd,
- but::const_string explanation)
- {
- m_Upper->log_exception(ostr, lcd, explanation);
- }
-+#endif
-
- void
- CNcbiBoostLogger::log_entry_start(ostream& ostr, but::log_entry_data const& led,
-@@ -1631,9 +1714,74 @@ NcbiTestGetUnit(CTempString test_name)
- END_NCBI_SCOPE
-
-
-+using namespace but;
-+
- /// Global initialization function called from Boost framework
--but::test_suite*
-+test_suite*
- init_unit_test_suite(int argc, char* argv[])
- {
- return NCBI_NS_NCBI::s_GetTestApp().InitTestFramework(argc, argv);
- }
-+
-+// This main() is mostly a copy from Boost's unit_test_main.ipp
-+int
-+main(int argc, char* argv[])
-+{
-+ int result = boost::exit_success;
-+
-+ try {
-+ framework::init( &init_unit_test_suite, argc, argv );
-+
-+ if( !runtime_config::test_to_run().is_empty() ) {
-+ test_case_filter filter( runtime_config::test_to_run() );
-+
-+ traverse_test_tree( framework::master_test_suite().p_id, filter );
-+ }
-+
-+ framework::run();
-+
-+ // Let's try to make report in case of any error after all catches.
-+ //results_reporter::make_report();
-+
-+ if (!runtime_config::no_result_code()) {
-+ result = results_collector.results( framework::master_test_suite().p_id ).result_code();
-+ if (!NCBI_NS_NCBI::s_GetTestApp().HasTestErrors()
-+ && NCBI_NS_NCBI::s_GetTestApp().HasTestTimeouts())
-+ {
-+ // This should certainly go to the output. So we can use only
-+ // printf, nothing else.
-+ printf("There were no test failures, only timeouts.\n"
-+ " (for autobuild scripts: NCBI_UNITTEST_TIMEOUTS_BUT_NO_ERRORS)\n");
-+ }
-+ }
-+ }
-+#if BOOST_VERSION >= 104200
-+ catch( framework::nothing_to_test const& ) {
-+ result = boost::exit_success;
-+ }
-+#endif
-+ catch( framework::internal_error const& ex ) {
-+ results_reporter::get_stream() << "Boost.Test framework internal error: " << ex.what() << std::endl;
-+
-+ result = boost::exit_exception_failure;
-+ }
-+ catch( framework::setup_error const& ex ) {
-+ results_reporter::get_stream() << "Test setup error: " << ex.what() << std::endl;
-+
-+ result = boost::exit_exception_failure;
-+ }
-+ catch( std::exception const& ex ) {
-+ results_reporter::get_stream() << "Test framework error: " << ex.what() << std::endl;
-+
-+ result = boost::exit_exception_failure;
-+ }
-+ catch( ... ) {
-+ results_reporter::get_stream() << "Boost.Test framework internal error: unknown reason" << std::endl;
-+
-+ result = boost::exit_exception_failure;
-+ }
-+
-+ results_reporter::make_report();
-+
-+ return result;
-+}
-diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-index 92e817f..cfab8ab 100644
---- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-@@ -1199,7 +1199,7 @@ private:
- CSeqDBAtlasHolder m_AtlasHolder;
-
- /// Reference to memory management layer.
-- mutable CSeqDBAtlas & m_Atlas;
-+ CSeqDBAtlas & m_Atlas;
-
- /// The list of database names provided to the constructor.
- string m_DBNames;
-diff --git a/c++/src/serial/stdtypes.cpp b/c++/src/serial/stdtypes.cpp
-index f6fa651..d6e8f80 100644
---- a/c++/src/serial/stdtypes.cpp
-+++ b/c++/src/serial/stdtypes.cpp
-@@ -720,7 +720,7 @@ public:
- 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 @@ public:
- // 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 @@ public:
- 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 @@ public:
- // unsigned -> signed
- if ( sizeof(value) == sizeof(result) ) {
- // same size - check for sign change only
-- if ( IsNegative(result) )
-+ if ( CParent::IsNegative(result) )
- ThrowIntegerOverflow();
- }
- }
diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild
index db7c5a24691..72c740fd30e 100644
--- a/sci-biology/rmblast/rmblast-1.2-r1.ebuild
+++ b/sci-biology/rmblast/rmblast-1.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -9,7 +9,8 @@ MY_NCBI_BLAST_V=2.2.23+
DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+"
HOMEPAGE="http://www.repeatmasker.org/RMBlast.html"
-SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz"
+SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz
+ https://dev.gentoo.org/~mgorny/dist/${P}-gcc47.patch.bz2"
LICENSE="OSL-2.1"
SLOT="0"
@@ -30,7 +31,7 @@ src_prepare() {
-e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \
-e 's/2.95\* | 2.96\* | 3\.\* | 4\.\* )/2.95\* | 2.96\* | \[3-9\]\.\* )/g' \
-i src/build-system/configure || die
- epatch "${FILESDIR}"/${P}-gcc47.patch
+ epatch "${WORKDIR}"/${P}-gcc47.patch
}
src_configure() {