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gentoo-overlay/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch

866 lines
31 KiB
Raw Blame History

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();
}
}
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