sci-biology/rmblast: [QA] Move patch to a distfile

Closes: https://bugs.gentoo.org/620616

3 files changed, 6 insertions, 869 deletions

diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest
index 00c455fce326..383d30fdb026 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 70200d59ea4a..000000000000
--- 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 db7c5a246910..72c740fd30e3 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() {