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commit: 930e41812a61debf91ffa4ccd81853567464962c |
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Author: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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AuthorDate: Sat Dec 9 23:22:44 2017 +0000 |
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Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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CommitDate: Sun Dec 10 00:05:29 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=930e4181 |
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|
8 |
sci-biology/rmblast: [QA] Move patch to a distfile |
9 |
|
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Closes: https://bugs.gentoo.org/620616 |
11 |
|
12 |
sci-biology/rmblast/Manifest | 3 +- |
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sci-biology/rmblast/files/rmblast-1.2-gcc47.patch | 865 ---------------------- |
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sci-biology/rmblast/rmblast-1.2-r1.ebuild | 7 +- |
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3 files changed, 6 insertions(+), 869 deletions(-) |
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|
17 |
diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest |
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index 00c455fce32..383d30fdb02 100644 |
19 |
--- a/sci-biology/rmblast/Manifest |
20 |
+++ b/sci-biology/rmblast/Manifest |
21 |
@@ -1 +1,2 @@ |
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-DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 SHA256 996be9886189364fff8ed39d4668122b2e5b8b010be47d929602416d95628eef SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 WHIRLPOOL aa3ada4297812a97614b0fe218de65d7474edfb5910e156eb09b625d45338a97b35f46876f5edf6105ead8b321a28f55ed7de2ad251bbc48ffd0cfa65ee2ac7a |
23 |
+DIST rmblast-1.2-gcc47.patch.bz2 7803 BLAKE2B cd3bb1aa2b6eb9e188f28589d42ce91f027866d91013f2a6123ee61e7ce28f980b858e775bc15313cf1573f0bc827f9e663d46c1bd0d2fe218745cfbbc3781a1 SHA512 4cd72dd5c777ad866b9cf674384872de5424404b524ac536e58ab412b98b6601aa5f609d05ea2329b77f16e7aca215bbc6eb3531652e5fe81e48cf997b56d13b |
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+DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 BLAKE2B 6539ec8fcd345bcc1c3ecede6acec233cdc343c3df18748e195dc525f4a65fefeee8398471a26dc671bfed8612e010c26b7a8a66a3c7198f142c2e068ff72751 SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 |
25 |
|
26 |
diff --git a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch |
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deleted file mode 100644 |
28 |
index 70200d59ea4..00000000000 |
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--- a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch |
30 |
+++ /dev/null |
31 |
@@ -1,865 +0,0 @@ |
32 |
- c++/include/corelib/ncbiexpt.hpp | 4 +- |
33 |
- c++/include/corelib/ncbimisc.hpp | 2 + |
34 |
- c++/include/corelib/ncbiobj.hpp | 2 +- |
35 |
- c++/include/corelib/ncbistl.hpp | 6 +- |
36 |
- c++/include/corelib/ncbistr.hpp | 2 +- |
37 |
- c++/include/corelib/test_boost.hpp | 44 +++++- |
38 |
- c++/include/dbapi/driver/dbapi_object_convert.hpp | 8 +- |
39 |
- .../dbapi/driver/impl/dbapi_driver_utils.hpp | 2 +- |
40 |
- c++/include/serial/impl/stltypes.hpp | 16 ++- |
41 |
- c++/include/serial/iterator.hpp | 6 +- |
42 |
- c++/include/serial/serialbase.hpp | 8 +- |
43 |
- c++/include/util/bitset/bmfunc.h | 7 + |
44 |
- c++/include/util/linkedset.hpp | 16 +-- |
45 |
- c++/include/util/rangemap.hpp | 4 +- |
46 |
- c++/src/connect/ncbi_gnutls.c | 19 ++- |
47 |
- c++/src/corelib/ncbifile.cpp | 2 +- |
48 |
- c++/src/corelib/test_boost.cpp | 156 ++++++++++++++++++++- |
49 |
- c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 2 +- |
50 |
- c++/src/serial/stdtypes.cpp | 8 +- |
51 |
- 19 files changed, 269 insertions(+), 45 deletions(-) |
52 |
- |
53 |
-diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp |
54 |
-index a9cf850..6d90e74 100644 |
55 |
---- a/c++/include/corelib/ncbiexpt.hpp |
56 |
-+++ b/c++/include/corelib/ncbiexpt.hpp |
57 |
-@@ -831,7 +831,7 @@ const TTo* UppermostCast(const TFrom& from) |
58 |
- exception_class(const exception_class& other) \ |
59 |
- : base_class(other) \ |
60 |
- { \ |
61 |
-- x_Assign(other); \ |
62 |
-+ this->x_Assign(other); \ |
63 |
- } \ |
64 |
- public: \ |
65 |
- virtual ~exception_class(void) throw() {} \ |
66 |
-@@ -1154,7 +1154,7 @@ public: |
67 |
- : TBase( other) |
68 |
- { |
69 |
- m_Errno = other.m_Errno; |
70 |
-- x_Assign(other); |
71 |
-+ this->x_Assign(other); |
72 |
- } |
73 |
- |
74 |
- /// Destructor. |
75 |
-diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp |
76 |
-index f45d280..f0c030d 100644 |
77 |
---- a/c++/include/corelib/ncbimisc.hpp |
78 |
-+++ b/c++/include/corelib/ncbimisc.hpp |
79 |
-@@ -57,6 +57,8 @@ |
80 |
- * @{ |
81 |
- */ |
82 |
- |
83 |
-+#include <stdlib.h> |
84 |
-+ |
85 |
- #ifndef NCBI_ESWITCH_DEFINED |
86 |
- #define NCBI_ESWITCH_DEFINED |
87 |
- |
88 |
-diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp |
89 |
-index 4f83db4..815c188 100644 |
90 |
---- a/c++/include/corelib/ncbiobj.hpp |
91 |
-+++ b/c++/include/corelib/ncbiobj.hpp |
92 |
-@@ -2128,7 +2128,7 @@ public: |
93 |
- CIRef<Interface, TThisType> ref( |
94 |
- dynamic_cast<Interface*>(proxy->GetLockedObject()), *this); |
95 |
- if (ref.NotNull()) { |
96 |
-- Unlock(ref.GetPointer()); |
97 |
-+ this->Unlock(ref.GetPointer()); |
98 |
- } |
99 |
- return ref; |
100 |
- } |
101 |
-diff --git a/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp |
102 |
-index 0bf465a..0618d9d 100644 |
103 |
---- a/c++/include/corelib/ncbistl.hpp |
104 |
-+++ b/c++/include/corelib/ncbistl.hpp |
105 |
-@@ -37,7 +37,6 @@ |
106 |
- |
107 |
- #include <common/ncbi_export.h> |
108 |
- |
109 |
-- |
110 |
- // Get rid of some warnings in MSVC++ 6.00 |
111 |
- #if (_MSC_VER >= 1200) |
112 |
- // too long identificator name in the debug info; truncated |
113 |
-@@ -162,6 +161,9 @@ typedef int NCBI_NAME2(T_EAT_SEMICOLON_,UniqueName) |
114 |
- #endif |
115 |
- |
116 |
- #if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_WORKSHOP) |
117 |
-+# if defined(NCBI_COMPILER_GCC) && NCBI_COMPILER_VERSION >= 400 |
118 |
-+# include <algorithm> |
119 |
-+# endif |
120 |
- // This template is used by some stl algorithms (sort, reverse...) |
121 |
- // We need to have our own implementation because some C++ Compiler vendors |
122 |
- // implemented it by using a temporary variable and an assignment operator |
123 |
-@@ -174,7 +176,7 @@ template<typename Iter> |
124 |
- inline |
125 |
- void iter_swap( Iter it1, Iter it2 ) |
126 |
- { |
127 |
-- swap( *it1, * it2 ); |
128 |
-+ swap( *it1, *it2 ); |
129 |
- } |
130 |
- |
131 |
- END_STD_SCOPE |
132 |
-diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp |
133 |
-index db7054f..63e3299 100644 |
134 |
---- a/c++/include/corelib/ncbistr.hpp |
135 |
-+++ b/c++/include/corelib/ncbistr.hpp |
136 |
-@@ -2583,7 +2583,7 @@ public: |
137 |
- : TBase(other) |
138 |
- { |
139 |
- m_Pos = other.m_Pos; |
140 |
-- x_Assign(other); |
141 |
-+ this->x_Assign(other); |
142 |
- } |
143 |
- |
144 |
- /// Destructor. |
145 |
-diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp |
146 |
-index 69c41f3..4cd77d3 100644 |
147 |
---- a/c++/include/corelib/test_boost.hpp |
148 |
-+++ b/c++/include/corelib/test_boost.hpp |
149 |
-@@ -56,10 +56,18 @@ |
150 |
- # undef BOOST_AUTO_TEST_MAIN |
151 |
- #endif |
152 |
- |
153 |
-+#ifdef NCBI_COMPILER_MSVC |
154 |
-+# pragma warning(push) |
155 |
-+// 'class' : class has virtual functions, but destructor is not virtual |
156 |
-+# pragma warning(disable: 4265) |
157 |
-+#endif |
158 |
-+ |
159 |
-+#include <boost/version.hpp> |
160 |
- #include <boost/test/auto_unit_test.hpp> |
161 |
- #include <boost/test/floating_point_comparison.hpp> |
162 |
- #include <boost/test/framework.hpp> |
163 |
- #include <boost/test/execution_monitor.hpp> |
164 |
-+#include <boost/test/parameterized_test.hpp> |
165 |
- |
166 |
- #include <boost/preprocessor/tuple/rem.hpp> |
167 |
- #include <boost/preprocessor/repeat.hpp> |
168 |
-@@ -72,6 +80,7 @@ |
169 |
- #undef BOOST_CHECK_THROW_IMPL |
170 |
- #undef BOOST_CHECK_NO_THROW_IMPL |
171 |
- #undef BOOST_FIXTURE_TEST_CASE |
172 |
-+#undef BOOST_PARAM_TEST_CASE |
173 |
- |
174 |
- #define BOOST_CHECK_THROW_IMPL( S, E, P, prefix, TL ) \ |
175 |
- try { \ |
176 |
-@@ -109,6 +118,12 @@ catch( ... ) { \ |
177 |
- } \ |
178 |
- /**/ |
179 |
- |
180 |
-+#if BOOST_VERSION >= 104200 |
181 |
-+# define NCBI_BOOST_LOCATION() , boost::execution_exception::location() |
182 |
-+#else |
183 |
-+# define NCBI_BOOST_LOCATION() |
184 |
-+#endif |
185 |
-+ |
186 |
- #define BOOST_FIXTURE_TEST_CASE( test_name, F ) \ |
187 |
- struct test_name : public F { void test_method(); }; \ |
188 |
- \ |
189 |
-@@ -124,7 +139,8 @@ static void BOOST_AUTO_TC_INVOKER( test_name )() \ |
190 |
- ::framework::current_test_case().p_name \ |
191 |
- << "\"" << ex); \ |
192 |
- throw boost::execution_exception( \ |
193 |
-- boost::execution_exception::cpp_exception_error, ""); \ |
194 |
-+ boost::execution_exception::cpp_exception_error, "" \ |
195 |
-+ NCBI_BOOST_LOCATION() ); \ |
196 |
- } \ |
197 |
- } \ |
198 |
- \ |
199 |
-@@ -142,6 +158,12 @@ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \ |
200 |
- void test_name::test_method() \ |
201 |
- /**/ |
202 |
- |
203 |
-+#define BOOST_PARAM_TEST_CASE( function, begin, end ) \ |
204 |
-+ ::NCBI_NS_NCBI::NcbiTestGenTestCases( function, \ |
205 |
-+ BOOST_TEST_STRINGIZE( function ), \ |
206 |
-+ (begin), (end) ) \ |
207 |
-+/**/ |
208 |
-+ |
209 |
- /// Set timeout value for the test case created using auto-registration |
210 |
- /// facility. |
211 |
- #define BOOST_AUTO_TEST_CASE_TIMEOUT(test_name, n) \ |
212 |
-@@ -158,6 +180,26 @@ static struct BOOST_JOIN( test_name, _timeout_spec ) \ |
213 |
- } BOOST_JOIN( test_name, _timeout_spec_inst ); \ |
214 |
- /**/ |
215 |
- |
216 |
-+/// Automatic registration of the set of test cases based on some function |
217 |
-+/// accepting one parameter. Set of parameters used to call that function is |
218 |
-+/// taken from iterator 'begin' which is incremented until it reaches 'end'. |
219 |
-+/// |
220 |
-+/// @sa BOOST_PARAM_TEST_CASE |
221 |
-+#define BOOST_AUTO_PARAM_TEST_CASE( function, begin, end ) \ |
222 |
-+ BOOST_AUTO_TU_REGISTRAR(function) ( \ |
223 |
-+ BOOST_PARAM_TEST_CASE(function, begin, end)) \ |
224 |
-+/**/ |
225 |
-+ |
226 |
-+#define BOOST_TIMEOUT(M) \ |
227 |
-+ do { \ |
228 |
-+ static string s(M); \ |
229 |
-+ throw boost::execution_exception( \ |
230 |
-+ boost::execution_exception::timeout_error, s \ |
231 |
-+ NCBI_BOOST_LOCATION()); \ |
232 |
-+ } while (0) \ |
233 |
-+/**/ |
234 |
-+ |
235 |
-+ |
236 |
- |
237 |
- #define NCBITEST_CHECK_IMPL(P, check_descr, TL, CT) \ |
238 |
- BOOST_CHECK_NO_THROW_IMPL(BOOST_CHECK_IMPL(P, check_descr, TL, CT), TL) |
239 |
-diff --git a/c++/include/dbapi/driver/dbapi_object_convert.hpp b/c++/include/dbapi/driver/dbapi_object_convert.hpp |
240 |
-index 6fcde61..eddde81 100644 |
241 |
---- a/c++/include/dbapi/driver/dbapi_object_convert.hpp |
242 |
-+++ b/c++/include/dbapi/driver/dbapi_object_convert.hpp |
243 |
-@@ -67,7 +67,7 @@ public: |
244 |
- operator const CTime&(void) const; |
245 |
- |
246 |
- private: |
247 |
-- mutable obj_type& m_Value; |
248 |
-+ obj_type& m_Value; |
249 |
- }; |
250 |
- |
251 |
- //////////////////////////////////////////////////////////////////////////////// |
252 |
-@@ -92,7 +92,7 @@ public: |
253 |
- operator const CTime&(void) const; |
254 |
- |
255 |
- private: |
256 |
-- mutable obj_type& m_Value; |
257 |
-+ obj_type& m_Value; |
258 |
- }; |
259 |
- |
260 |
- //////////////////////////////////////////////////////////////////////////////// |
261 |
-@@ -133,7 +133,7 @@ public: |
262 |
- operator const CTime&(void) const; |
263 |
- |
264 |
- private: |
265 |
-- mutable obj_type& m_Value; |
266 |
-+ obj_type& m_Value; |
267 |
- }; |
268 |
- |
269 |
- //////////////////////////////////////////////////////////////////////////////// |
270 |
-@@ -174,7 +174,7 @@ public: |
271 |
- operator const CTime&(void) const; |
272 |
- |
273 |
- private: |
274 |
-- mutable obj_type& m_Value; |
275 |
-+ obj_type& m_Value; |
276 |
- }; |
277 |
- |
278 |
- //////////////////////////////////////////////////////////////////////////////// |
279 |
-diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp |
280 |
-index 0792a6d..b6bd64b 100644 |
281 |
---- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp |
282 |
-+++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp |
283 |
-@@ -231,7 +231,7 @@ protected: |
284 |
- |
285 |
- private: |
286 |
- const string& m_SPName; |
287 |
-- mutable impl::CConnection& m_Conn; |
288 |
-+ impl::CConnection& m_Conn; |
289 |
- }; |
290 |
- |
291 |
- |
292 |
-diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp |
293 |
-index d41ab94..7d9e3ce 100644 |
294 |
---- a/c++/include/serial/impl/stltypes.hpp |
295 |
-+++ b/c++/include/serial/impl/stltypes.hpp |
296 |
-@@ -412,6 +412,7 @@ public: |
297 |
- typedef StlIterator TStlIterator; |
298 |
- typedef TypeInfoIterator TTypeInfoIterator; |
299 |
- typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr; |
300 |
-+ typedef CStlClassInfoFunctions<Container> CParent; |
301 |
- |
302 |
- static TStlIterator& It(TTypeInfoIterator& iter) |
303 |
- { |
304 |
-@@ -437,7 +438,8 @@ public: |
305 |
- } |
306 |
- static bool InitIterator(TTypeInfoIterator& iter) |
307 |
- { |
308 |
-- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin(); |
309 |
-+ TStlIterator stl_iter |
310 |
-+ = CParent::Get(iter.GetContainerPtr()).begin(); |
311 |
- if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) { |
312 |
- void* data = &iter.m_IteratorData; |
313 |
- new (data) TStlIterator(stl_iter); |
314 |
-@@ -445,7 +447,7 @@ public: |
315 |
- else { |
316 |
- iter.m_IteratorData = new TStlIterator(stl_iter); |
317 |
- } |
318 |
-- return stl_iter != Get(iter.GetContainerPtr()).end(); |
319 |
-+ return stl_iter != CParent::Get(iter.GetContainerPtr()).end(); |
320 |
- } |
321 |
- static void ReleaseIterator(TTypeInfoIterator& iter) |
322 |
- { |
323 |
-@@ -466,7 +468,7 @@ public: |
324 |
- |
325 |
- static bool NextElement(TTypeInfoIterator& iter) |
326 |
- { |
327 |
-- return ++It(iter) != Get(iter.GetContainerPtr()).end(); |
328 |
-+ return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end(); |
329 |
- } |
330 |
- static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter) |
331 |
- { |
332 |
-@@ -503,7 +505,7 @@ public: |
333 |
- |
334 |
- static bool EraseElement(TTypeInfoIterator& iter) |
335 |
- { |
336 |
-- TStlIterator& it = It(iter); |
337 |
-+ TStlIterator& it = CParent::It(iter); |
338 |
- Container* c = static_cast<Container*>(iter.GetContainerPtr()); |
339 |
- it = c->erase(it); |
340 |
- return it != c->end(); |
341 |
-@@ -511,7 +513,7 @@ public: |
342 |
- static void EraseAllElements(TTypeInfoIterator& iter) |
343 |
- { |
344 |
- Container* c = static_cast<Container*>(iter.GetContainerPtr()); |
345 |
-- c->erase(It(iter), c->end()); |
346 |
-+ c->erase(CParent::It(iter), c->end()); |
347 |
- } |
348 |
- |
349 |
- static void SetIteratorFunctions(CStlOneArgTemplate* info) |
350 |
-@@ -542,7 +544,7 @@ public: |
351 |
- } |
352 |
- static bool EraseElement(TTypeInfoIterator& iter) |
353 |
- { |
354 |
-- TStlIterator& it = It(iter); |
355 |
-+ TStlIterator& it = CParent::It(iter); |
356 |
- Container* c = static_cast<Container*>(iter.GetContainerPtr()); |
357 |
- TStlIterator erase = it++; |
358 |
- c->erase(erase); |
359 |
-@@ -551,7 +553,7 @@ public: |
360 |
- static void EraseAllElements(TTypeInfoIterator& iter) |
361 |
- { |
362 |
- Container* c = static_cast<Container*>(iter.GetContainerPtr()); |
363 |
-- c->erase(It(iter), c->end()); |
364 |
-+ c->erase(CParent::It(iter), c->end()); |
365 |
- } |
366 |
- |
367 |
- static void SetIteratorFunctions(CStlOneArgTemplate* info) |
368 |
-diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp |
369 |
-index 25e1193..cddb046 100644 |
370 |
---- a/c++/include/serial/iterator.hpp |
371 |
-+++ b/c++/include/serial/iterator.hpp |
372 |
-@@ -491,13 +491,13 @@ protected: |
373 |
- CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo) |
374 |
- : m_NeedType(needType) |
375 |
- { |
376 |
-- Init(beginInfo); |
377 |
-+ this->Init(beginInfo); |
378 |
- } |
379 |
- CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo, |
380 |
- const string& filter) |
381 |
- : m_NeedType(needType) |
382 |
- { |
383 |
-- Init(beginInfo, filter); |
384 |
-+ this->Init(beginInfo, filter); |
385 |
- } |
386 |
- |
387 |
- virtual bool CanSelect(const CConstObjectInfo& object) |
388 |
-@@ -599,7 +599,7 @@ public: |
389 |
- |
390 |
- CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo) |
391 |
- { |
392 |
-- Init(beginInfo); |
393 |
-+ this->Init(beginInfo); |
394 |
- return *this; |
395 |
- } |
396 |
- |
397 |
-diff --git a/c++/include/serial/serialbase.hpp b/c++/include/serial/serialbase.hpp |
398 |
-index be6a4f9..d59fb25 100644 |
399 |
---- a/c++/include/serial/serialbase.hpp |
400 |
-+++ b/c++/include/serial/serialbase.hpp |
401 |
-@@ -364,11 +364,15 @@ public: |
402 |
- // cast to object type |
403 |
- TObject& operator*(void) |
404 |
- { |
405 |
-- return *reinterpret_cast<TObject*>(m_Buffer); |
406 |
-+ TObject* ptr = static_cast<TObject*> |
407 |
-+ (static_cast<void*>(m_Buffer)); |
408 |
-+ return *ptr; |
409 |
- } |
410 |
- const TObject& operator*(void) const |
411 |
- { |
412 |
-- return *reinterpret_cast<const TObject*>(m_Buffer); |
413 |
-+ const TObject* ptr = static_cast<const TObject*> |
414 |
-+ (static_cast<const void*>(m_Buffer)); |
415 |
-+ return *ptr; |
416 |
- } |
417 |
- |
418 |
- // construct/destruct object |
419 |
-diff --git a/c++/include/util/bitset/bmfunc.h b/c++/include/util/bitset/bmfunc.h |
420 |
-index 5917ee5..a8c204b 100644 |
421 |
---- a/c++/include/util/bitset/bmfunc.h |
422 |
-+++ b/c++/include/util/bitset/bmfunc.h |
423 |
-@@ -37,6 +37,13 @@ For more information please visit: http://bmagic.sourceforge.net |
424 |
- namespace bm |
425 |
- { |
426 |
- |
427 |
-+bm::id_t bit_block_any_range(const bm::word_t* block, |
428 |
-+ bm::word_t left, |
429 |
-+ bm::word_t right); |
430 |
-+ |
431 |
-+bm::id_t bit_block_calc_count_range(const bm::word_t* block, |
432 |
-+ bm::word_t left, |
433 |
-+ bm::word_t right); |
434 |
- |
435 |
- /*! |
436 |
- @brief Structure with statistical information about bitset's memory |
437 |
-diff --git a/c++/include/util/linkedset.hpp b/c++/include/util/linkedset.hpp |
438 |
-index e8bbe6e..364164b 100644 |
439 |
---- a/c++/include/util/linkedset.hpp |
440 |
-+++ b/c++/include/util/linkedset.hpp |
441 |
-@@ -268,10 +268,10 @@ public: |
442 |
- pair<iterator, bool> ins = m_Container.insert(value); |
443 |
- if ( ins.second ) { |
444 |
- if ( ins.first == begin() ) |
445 |
-- insertToStart(*ins.first); |
446 |
-+ this->insertToStart(*ins.first); |
447 |
- else { |
448 |
- iterator prev = ins.first; |
449 |
-- insertAfter(*--prev, *ins.first); |
450 |
-+ this->insertAfter(*--prev, *ins.first); |
451 |
- } |
452 |
- } |
453 |
- return ins; |
454 |
-@@ -280,10 +280,10 @@ public: |
455 |
- void erase(iterator iter) |
456 |
- { |
457 |
- if ( iter == begin() ) |
458 |
-- removeFromStart(*iter); |
459 |
-+ this->removeFromStart(*iter); |
460 |
- else { |
461 |
- iterator prev = iter; |
462 |
-- removeAfter(*--prev, *iter); |
463 |
-+ this->removeAfter(*--prev, *iter); |
464 |
- } |
465 |
- m_Container.erase(iter); |
466 |
- } |
467 |
-@@ -422,10 +422,10 @@ public: |
468 |
- { |
469 |
- iterator iter = m_Container.insert(value); |
470 |
- if ( iter == begin() ) |
471 |
-- insertToStart(get(iter)); |
472 |
-+ this->insertToStart(get(iter)); |
473 |
- else { |
474 |
- iterator prev = iter; |
475 |
-- insertAfter(get(--prev), get(iter)); |
476 |
-+ this->insertAfter(get(--prev), get(iter)); |
477 |
- } |
478 |
- return iter; |
479 |
- } |
480 |
-@@ -433,10 +433,10 @@ public: |
481 |
- void erase(iterator iter) |
482 |
- { |
483 |
- if ( iter == begin() ) |
484 |
-- removeFromStart(get(iter)); |
485 |
-+ this->removeFromStart(get(iter)); |
486 |
- else { |
487 |
- iterator prev = iter; |
488 |
-- removeAfter(get(--prev), get(iter)); |
489 |
-+ this->removeAfter(get(--prev), get(iter)); |
490 |
- } |
491 |
- m_Container.erase(iter); |
492 |
- } |
493 |
-diff --git a/c++/include/util/rangemap.hpp b/c++/include/util/rangemap.hpp |
494 |
-index c4f5f37..56e267d 100644 |
495 |
---- a/c++/include/util/rangemap.hpp |
496 |
-+++ b/c++/include/util/rangemap.hpp |
497 |
-@@ -578,7 +578,7 @@ public: |
498 |
- // get level |
499 |
- |
500 |
- // insert element |
501 |
-- TSelectMapI selectIter = insertLevel(selectKey); |
502 |
-+ TSelectMapI selectIter = this->insertLevel(selectKey); |
503 |
- pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value); |
504 |
- |
505 |
- pair<iterator, bool> ret; |
506 |
-@@ -640,7 +640,7 @@ public: |
507 |
- // insert element |
508 |
- iterator ret; |
509 |
- ret.m_Range = range_type::GetWhole(); |
510 |
-- ret.m_SelectIter = insertLevel(selectKey); |
511 |
-+ ret.m_SelectIter = this->insertLevel(selectKey); |
512 |
- ret.m_SelectIterEnd = this->m_SelectMap.end(); |
513 |
- ret.m_LevelIter = ret.m_SelectIter->second.insert(value); |
514 |
- return ret; |
515 |
-diff --git a/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c |
516 |
-index f0242b7..8b13713 100644 |
517 |
---- a/c++/src/connect/ncbi_gnutls.c |
518 |
-+++ b/c++/src/connect/ncbi_gnutls.c |
519 |
-@@ -98,7 +98,6 @@ static const int kGnuTlsCertPrio[] = { |
520 |
- 0 |
521 |
- }; |
522 |
- static const int kGnuTlsCompPrio[] = { |
523 |
-- GNUTLS_COMP_LZO, |
524 |
- GNUTLS_COMP_ZLIB, |
525 |
- GNUTLS_COMP_NULL, |
526 |
- 0 |
527 |
-@@ -254,6 +253,24 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error) |
528 |
- } |
529 |
- |
530 |
- |
531 |
-+/*ARGSUSED*/ |
532 |
-+static void x_set_errno(gnutls_session_t session, int error) |
533 |
-+{ |
534 |
-+# ifdef LIBGNUTLS_VERSION_NUMBER |
535 |
-+# if \ |
536 |
-+ LIBGNUTLS_VERSION_MAJOR > 1 || \ |
537 |
-+ LIBGNUTLS_VERSION_MINOR > 5 || \ |
538 |
-+ LIBGNUTLS_VERSION_PATCH > 3 |
539 |
-+ gnutls_transport_set_errno(session, error); |
540 |
-+ return; |
541 |
-+# endif /*LIBGNUTLS_VERSION >= 1.5.4*/ |
542 |
-+# endif /*LIBGNUTLS_VERSION_NUMBER*/ |
543 |
-+ /*NOTREACHED*/ |
544 |
-+ if (error) |
545 |
-+ errno = error; |
546 |
-+} |
547 |
-+ |
548 |
-+ |
549 |
- static ssize_t x_GnuTlsPull(gnutls_transport_ptr_t ptr, |
550 |
- void* buf, size_t size) |
551 |
- { |
552 |
-diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp |
553 |
-index d751e62..fdc81c7 100644 |
554 |
---- a/c++/src/corelib/ncbifile.cpp |
555 |
-+++ b/c++/src/corelib/ncbifile.cpp |
556 |
-@@ -51,8 +51,8 @@ |
557 |
- # include <dirent.h> |
558 |
- # include <pwd.h> |
559 |
- # include <fcntl.h> |
560 |
--# include <sys/time.h> |
561 |
- # include <sys/mman.h> |
562 |
-+# include <sys/time.h> |
563 |
- # ifdef HAVE_SYS_STATVFS_H |
564 |
- # include <sys/statvfs.h> |
565 |
- # endif |
566 |
-diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp |
567 |
-index dfd9cc8..f93d2ca 100644 |
568 |
---- a/c++/src/corelib/test_boost.cpp |
569 |
-+++ b/c++/src/corelib/test_boost.cpp |
570 |
-@@ -41,6 +41,7 @@ |
571 |
- #ifndef BOOST_TEST_NO_LIB |
572 |
- # define BOOST_TEST_NO_LIB |
573 |
- #endif |
574 |
-+#define BOOST_TEST_NO_MAIN |
575 |
- #include <corelib/test_boost.hpp> |
576 |
- |
577 |
- #include <boost/preprocessor/cat.hpp> |
578 |
-@@ -95,6 +96,7 @@ const char* kTestResultTimeout = "timeout"; |
579 |
- const char* kTestResultAborted = "aborted"; |
580 |
- const char* kTestResultSkipped = "skipped"; |
581 |
- const char* kTestResultDisabled = "disabled"; |
582 |
-+const char* kTestResultToFix = "tofix"; |
583 |
- |
584 |
- |
585 |
- typedef but::results_reporter::format TBoostRepFormatter; |
586 |
-@@ -168,14 +170,24 @@ public: |
587 |
- unsigned long elapsed); |
588 |
- virtual |
589 |
- void test_unit_skipped(ostream& ostr, but::test_unit const& tu); |
590 |
-+#if BOOST_VERSION >= 104200 |
591 |
-+ virtual |
592 |
-+ void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd, |
593 |
-+ boost::execution_exception const& ex); |
594 |
-+ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up |
595 |
-+ using TBoostLogFormatter::log_exception; |
596 |
-+#else |
597 |
- virtual |
598 |
- void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd, |
599 |
- but::const_string explanation); |
600 |
-+#endif |
601 |
- virtual |
602 |
- void log_entry_start (ostream& ostr, but::log_entry_data const& led, |
603 |
- log_entry_types let); |
604 |
- virtual |
605 |
- void log_entry_value (ostream& ostr, but::const_string value); |
606 |
-+ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up |
607 |
-+ using TBoostLogFormatter::log_entry_value; |
608 |
- virtual |
609 |
- void log_entry_finish (ostream& ostr); |
610 |
- |
611 |
-@@ -402,10 +414,15 @@ public: |
612 |
- |
613 |
- /// Mark test case as failed due to hit of the timeout |
614 |
- void SetTestTimedOut(but::test_case* tc); |
615 |
-+ /// Register the fact of test failure |
616 |
-+ void SetTestErrored(but::test_case* tc); |
617 |
-+ /// Check if given test is marked as requiring fixing in the future |
618 |
-+ bool IsTestToFix(const but::test_unit* tu); |
619 |
- |
620 |
- /// Get number of actually executed tests |
621 |
- int GetRanTestsCount(void); |
622 |
-- |
623 |
-+ /// Get number of tests that were failed but are marked to be fixed |
624 |
-+ int GetToFixTestsCount(void); |
625 |
- /// Get string representation of result of test execution |
626 |
- string GetTestResultString(but::test_unit* tu); |
627 |
- |
628 |
-@@ -415,6 +432,11 @@ public: |
629 |
- /// Check if user initialization functions failed |
630 |
- bool IsInitFailed(void); |
631 |
- |
632 |
-+ /// Check if there were any test errors |
633 |
-+ bool HasTestErrors(void); |
634 |
-+ /// Check if there were any timeouted tests |
635 |
-+ bool HasTestTimeouts(void); |
636 |
-+ |
637 |
- private: |
638 |
- typedef list<TNcbiTestUserFunction> TUserFuncsList; |
639 |
- |
640 |
-@@ -493,6 +515,8 @@ private: |
641 |
- TUnitsSet m_DisabledTests; |
642 |
- /// List of all tests which result is a timeout |
643 |
- TUnitsSet m_TimedOutTests; |
644 |
-+ /// List of all tests marked as in need of fixing in the future |
645 |
-+ TUnitsSet m_ToFixTests; |
646 |
- /// List of all dependencies for each test having dependencies |
647 |
- TUnitToManyMap m_TestDeps; |
648 |
- /// Observer to make test dependencies and look for unit's timeouts |
649 |
-@@ -512,12 +536,18 @@ private: |
650 |
- /// String representation for whole test timeout (real value taken from |
651 |
- /// CHECK_TIMEOUT in Makefile). |
652 |
- string m_TimeoutStr; |
653 |
-+ /// Multiplicator for timeouts |
654 |
-+ double m_TimeMult; |
655 |
- /// Timer measuring elapsed time for the whole test |
656 |
- CStopWatch m_Timer; |
657 |
- /// Timeout that was set in currently executing unit before adjustment |
658 |
- /// |
659 |
- /// @sa AdjustTestTimeout() |
660 |
- unsigned int m_CurUnitTimeout; |
661 |
-+ /// Flag showing if there were some test errors |
662 |
-+ bool m_HasTestErrors; |
663 |
-+ /// Flag showing if there were some timeouted tests |
664 |
-+ bool m_HasTestTimeouts; |
665 |
- }; |
666 |
- |
667 |
- |
668 |
-@@ -794,7 +824,10 @@ CNcbiTestApplication::CNcbiTestApplication(void) |
669 |
- m_RunMode (0), |
670 |
- m_DummyTest(NULL), |
671 |
- m_Timeout (0), |
672 |
-- m_Timer (CStopWatch::eStart) |
673 |
-+ m_TimeMult (1), |
674 |
-+ m_Timer (CStopWatch::eStart), |
675 |
-+ m_HasTestErrors(false), |
676 |
-+ m_HasTestTimeouts(false) |
677 |
- { |
678 |
- m_Reporter = new CNcbiBoostReporter(); |
679 |
- m_Logger = new CNcbiBoostLogger(); |
680 |
-@@ -1244,6 +1277,24 @@ CNcbiTestApplication::GetRanTestsCount(void) |
681 |
- return result; |
682 |
- } |
683 |
- |
684 |
-+int |
685 |
-+CNcbiTestApplication::GetToFixTestsCount(void) |
686 |
-+{ |
687 |
-+ int result = 0; |
688 |
-+ ITERATE(TUnitsSet, it, m_ToFixTests) { |
689 |
-+ if (!but::results_collector.results((*it)->p_id).passed()) |
690 |
-+ ++result; |
691 |
-+ } |
692 |
-+ return result; |
693 |
-+} |
694 |
-+ |
695 |
-+inline bool |
696 |
-+CNcbiTestApplication::IsTestToFix(const but::test_unit* tu) |
697 |
-+{ |
698 |
-+ return m_ToFixTests.find(const_cast<but::test_unit*>(tu)) |
699 |
-+ != m_ToFixTests.end(); |
700 |
-+} |
701 |
-+ |
702 |
- inline void |
703 |
- CNcbiTestApplication::x_SetupBoostReporters(void) |
704 |
- { |
705 |
-@@ -1391,6 +1442,18 @@ CNcbiTestApplication::InitTestFramework(int argc, char* argv[]) |
706 |
- return NULL; |
707 |
- } |
708 |
- |
709 |
-+inline bool |
710 |
-+CNcbiTestApplication::HasTestErrors(void) |
711 |
-+{ |
712 |
-+ return m_HasTestErrors; |
713 |
-+} |
714 |
-+ |
715 |
-+inline bool |
716 |
-+CNcbiTestApplication::HasTestTimeouts(void) |
717 |
-+{ |
718 |
-+ return m_HasTestTimeouts; |
719 |
-+} |
720 |
-+ |
721 |
- void |
722 |
- CNcbiTestsCollector::visit(but::test_case const& test) |
723 |
- { |
724 |
-@@ -1431,9 +1494,20 @@ CNcbiTestsObserver::test_unit_finish(but::test_unit const& tu, |
725 |
- // elapsed comes in microseconds |
726 |
- if (timeout != 0 && timeout < elapsed / 1000000) { |
727 |
- boost::execution_exception ex( |
728 |
-- boost::execution_exception::timeout_error, "Timeout exceeded"); |
729 |
-+ boost::execution_exception::timeout_error, "Timeout exceeded" |
730 |
-+ NCBI_BOOST_LOCATION()); |
731 |
- but::framework::exception_caught(ex); |
732 |
- } |
733 |
-+ |
734 |
-+ but::test_results& tr = but::s_rc_impl().m_results_store[tu.p_id]; |
735 |
-+ if (!tr.passed() && s_GetTestApp().IsTestToFix(&tu)) { |
736 |
-+ static_cast<but::readwrite_property<bool>& >( |
737 |
-+ static_cast<but::class_property<bool>& >( |
738 |
-+ tr.p_skipped)).set(true); |
739 |
-+ static_cast<but::readwrite_property<but::counter_t>& >( |
740 |
-+ static_cast<but::class_property<but::counter_t>& >( |
741 |
-+ tr.p_assertions_failed)).set(0); |
742 |
-+ } |
743 |
- } |
744 |
- |
745 |
- void |
746 |
-@@ -1551,12 +1625,21 @@ CNcbiBoostLogger::test_unit_skipped(ostream& ostr, but::test_unit const& tu) |
747 |
- m_Upper->test_unit_skipped(ostr, tu); |
748 |
- } |
749 |
- |
750 |
-+#if BOOST_VERSION >= 104200 |
751 |
-+void |
752 |
-+CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd, |
753 |
-+ boost::execution_exception const& ex) |
754 |
-+{ |
755 |
-+ m_Upper->log_exception(ostr, lcd, ex); |
756 |
-+} |
757 |
-+#else |
758 |
- void |
759 |
- CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd, |
760 |
- but::const_string explanation) |
761 |
- { |
762 |
- m_Upper->log_exception(ostr, lcd, explanation); |
763 |
- } |
764 |
-+#endif |
765 |
- |
766 |
- void |
767 |
- CNcbiBoostLogger::log_entry_start(ostream& ostr, but::log_entry_data const& led, |
768 |
-@@ -1631,9 +1714,74 @@ NcbiTestGetUnit(CTempString test_name) |
769 |
- END_NCBI_SCOPE |
770 |
- |
771 |
- |
772 |
-+using namespace but; |
773 |
-+ |
774 |
- /// Global initialization function called from Boost framework |
775 |
--but::test_suite* |
776 |
-+test_suite* |
777 |
- init_unit_test_suite(int argc, char* argv[]) |
778 |
- { |
779 |
- return NCBI_NS_NCBI::s_GetTestApp().InitTestFramework(argc, argv); |
780 |
- } |
781 |
-+ |
782 |
-+// This main() is mostly a copy from Boost's unit_test_main.ipp |
783 |
-+int |
784 |
-+main(int argc, char* argv[]) |
785 |
-+{ |
786 |
-+ int result = boost::exit_success; |
787 |
-+ |
788 |
-+ try { |
789 |
-+ framework::init( &init_unit_test_suite, argc, argv ); |
790 |
-+ |
791 |
-+ if( !runtime_config::test_to_run().is_empty() ) { |
792 |
-+ test_case_filter filter( runtime_config::test_to_run() ); |
793 |
-+ |
794 |
-+ traverse_test_tree( framework::master_test_suite().p_id, filter ); |
795 |
-+ } |
796 |
-+ |
797 |
-+ framework::run(); |
798 |
-+ |
799 |
-+ // Let's try to make report in case of any error after all catches. |
800 |
-+ //results_reporter::make_report(); |
801 |
-+ |
802 |
-+ if (!runtime_config::no_result_code()) { |
803 |
-+ result = results_collector.results( framework::master_test_suite().p_id ).result_code(); |
804 |
-+ if (!NCBI_NS_NCBI::s_GetTestApp().HasTestErrors() |
805 |
-+ && NCBI_NS_NCBI::s_GetTestApp().HasTestTimeouts()) |
806 |
-+ { |
807 |
-+ // This should certainly go to the output. So we can use only |
808 |
-+ // printf, nothing else. |
809 |
-+ printf("There were no test failures, only timeouts.\n" |
810 |
-+ " (for autobuild scripts: NCBI_UNITTEST_TIMEOUTS_BUT_NO_ERRORS)\n"); |
811 |
-+ } |
812 |
-+ } |
813 |
-+ } |
814 |
-+#if BOOST_VERSION >= 104200 |
815 |
-+ catch( framework::nothing_to_test const& ) { |
816 |
-+ result = boost::exit_success; |
817 |
-+ } |
818 |
-+#endif |
819 |
-+ catch( framework::internal_error const& ex ) { |
820 |
-+ results_reporter::get_stream() << "Boost.Test framework internal error: " << ex.what() << std::endl; |
821 |
-+ |
822 |
-+ result = boost::exit_exception_failure; |
823 |
-+ } |
824 |
-+ catch( framework::setup_error const& ex ) { |
825 |
-+ results_reporter::get_stream() << "Test setup error: " << ex.what() << std::endl; |
826 |
-+ |
827 |
-+ result = boost::exit_exception_failure; |
828 |
-+ } |
829 |
-+ catch( std::exception const& ex ) { |
830 |
-+ results_reporter::get_stream() << "Test framework error: " << ex.what() << std::endl; |
831 |
-+ |
832 |
-+ result = boost::exit_exception_failure; |
833 |
-+ } |
834 |
-+ catch( ... ) { |
835 |
-+ results_reporter::get_stream() << "Boost.Test framework internal error: unknown reason" << std::endl; |
836 |
-+ |
837 |
-+ result = boost::exit_exception_failure; |
838 |
-+ } |
839 |
-+ |
840 |
-+ results_reporter::make_report(); |
841 |
-+ |
842 |
-+ return result; |
843 |
-+} |
844 |
-diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp |
845 |
-index 92e817f..cfab8ab 100644 |
846 |
---- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp |
847 |
-+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp |
848 |
-@@ -1199,7 +1199,7 @@ private: |
849 |
- CSeqDBAtlasHolder m_AtlasHolder; |
850 |
- |
851 |
- /// Reference to memory management layer. |
852 |
-- mutable CSeqDBAtlas & m_Atlas; |
853 |
-+ CSeqDBAtlas & m_Atlas; |
854 |
- |
855 |
- /// The list of database names provided to the constructor. |
856 |
- string m_DBNames; |
857 |
-diff --git a/c++/src/serial/stdtypes.cpp b/c++/src/serial/stdtypes.cpp |
858 |
-index f6fa651..d6e8f80 100644 |
859 |
---- a/c++/src/serial/stdtypes.cpp |
860 |
-+++ b/c++/src/serial/stdtypes.cpp |
861 |
-@@ -720,7 +720,7 @@ public: |
862 |
- if ( IsSigned() ) { |
863 |
- // signed -> unsigned |
864 |
- // check for negative value |
865 |
-- if ( IsNegative(value) ) |
866 |
-+ if ( CParent::IsNegative(value) ) |
867 |
- ThrowIntegerOverflow(); |
868 |
- } |
869 |
- if ( sizeof(value) > sizeof(result) ) { |
870 |
-@@ -751,7 +751,7 @@ public: |
871 |
- // unsigned -> signed |
872 |
- if ( sizeof(value) == sizeof(result) ) { |
873 |
- // same size - check for sign change only |
874 |
-- if ( IsNegative(result) ) |
875 |
-+ if ( CParent::IsNegative(result) ) |
876 |
- ThrowIntegerOverflow(); |
877 |
- } |
878 |
- } |
879 |
-@@ -786,7 +786,7 @@ public: |
880 |
- if ( IsSigned() ) { |
881 |
- // signed -> unsigned |
882 |
- // check for negative value |
883 |
-- if ( IsNegative(value) ) |
884 |
-+ if ( CParent::IsNegative(value) ) |
885 |
- ThrowIntegerOverflow(); |
886 |
- } |
887 |
- if ( sizeof(value) > sizeof(result) ) { |
888 |
-@@ -817,7 +817,7 @@ public: |
889 |
- // unsigned -> signed |
890 |
- if ( sizeof(value) == sizeof(result) ) { |
891 |
- // same size - check for sign change only |
892 |
-- if ( IsNegative(result) ) |
893 |
-+ if ( CParent::IsNegative(result) ) |
894 |
- ThrowIntegerOverflow(); |
895 |
- } |
896 |
- } |
897 |
|
898 |
diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild |
899 |
index db7c5a24691..72c740fd30e 100644 |
900 |
--- a/sci-biology/rmblast/rmblast-1.2-r1.ebuild |
901 |
+++ b/sci-biology/rmblast/rmblast-1.2-r1.ebuild |
902 |
@@ -1,4 +1,4 @@ |
903 |
-# Copyright 1999-2015 Gentoo Foundation |
904 |
+# Copyright 1999-2017 Gentoo Foundation |
905 |
# Distributed under the terms of the GNU General Public License v2 |
906 |
|
907 |
EAPI=5 |
908 |
@@ -9,7 +9,8 @@ MY_NCBI_BLAST_V=2.2.23+ |
909 |
|
910 |
DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+" |
911 |
HOMEPAGE="http://www.repeatmasker.org/RMBlast.html" |
912 |
-SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz" |
913 |
+SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz |
914 |
+ https://dev.gentoo.org/~mgorny/dist/${P}-gcc47.patch.bz2" |
915 |
|
916 |
LICENSE="OSL-2.1" |
917 |
SLOT="0" |
918 |
@@ -30,7 +31,7 @@ src_prepare() { |
919 |
-e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \ |
920 |
-e 's/2.95\* | 2.96\* | 3\.\* | 4\.\* )/2.95\* | 2.96\* | \[3-9\]\.\* )/g' \ |
921 |
-i src/build-system/configure || die |
922 |
- epatch "${FILESDIR}"/${P}-gcc47.patch |
923 |
+ epatch "${WORKDIR}"/${P}-gcc47.patch |
924 |
} |
925 |
|
926 |
src_configure() { |