[med-svn] [Git][med-team/hyphy][master] 2 commits: Refresh patches
Andreas Tille
gitlab at salsa.debian.org
Fri Dec 6 13:50:17 GMT 2019
Andreas Tille pushed to branch master at Debian Med / hyphy
Commits:
3554ad3e by Andreas Tille at 2019-12-06T12:42:44Z
Refresh patches
- - - - -
61765673 by Andreas Tille at 2019-12-06T13:49:53Z
Some patches for gcc9 - not finished yet
- - - - -
4 changed files:
- debian/patches/drop_profiling_option.patch
- + debian/patches/gcc9.patch
- debian/patches/series
- debian/patches/use_debian_sqlite.patch
Changes:
=====================================
debian/patches/drop_profiling_option.patch
=====================================
@@ -5,7 +5,7 @@ Bug-Debian: http://bugs.debian.org/793345
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -543,11 +543,11 @@ set_target_properties(
+@@ -544,11 +544,11 @@ set_target_properties(
HYPHYGTEST
PROPERTIES
if(${OPENMP_FOUND})
=====================================
debian/patches/gcc9.patch
=====================================
@@ -0,0 +1,229 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 06 Dec 2019 13:30:30 +0100
+Description: Fix Build issue with gcc9
+
+--- a/tests/gtests/ut_avllists.cpp
++++ b/tests/gtests/ut_avllists.cpp
+@@ -367,7 +367,7 @@ TEST_F(AVLListTest,toStrTest){
+ }
+
+ _String* return_str = (_String*)al.toStr();
+- EXPECT_STREQ("(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10)", return_str->getStr());
++ EXPECT_STREQ("(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10)", return_str->get_str());
+ }
+
+ TEST_F(AVLListTest,RetrieveTest) {
+@@ -562,7 +562,7 @@ TEST_F(AVLListXTest,PopulateFromListTest
+
+ alx.PopulateFromList(result_list);
+ _String* return_str = (_String*)alx.dataList->list_data[2];
+- EXPECT_STREQ("hyphy", return_str->getStr());
++ EXPECT_STREQ("hyphy", return_str->get_str());
+ }
+
+
+@@ -602,7 +602,7 @@ TEST_F(AVLListXLTest,SetAndGetXtraTest){
+ alxl.SetXtra(0,(BaseRef)xtra_str, false);
+
+ _String* x = (_String*)alxl.GetXtra((long)0);
+- EXPECT_STREQ("xtra",x->getStr());
++ EXPECT_STREQ("xtra",x->get_str());
+
+ }
+
+--- a/tests/gtests/ut_list.cpp
++++ b/tests/gtests/ut_list.cpp
+@@ -134,7 +134,7 @@ TEST_F(ListTest,_StackCopyConstructorLis
+ _List list = _List(str_list, 0, 4);
+
+ _String* return_str = (_String*)list[4];
+- EXPECT_STREQ("four", return_str->getStr());
++ EXPECT_STREQ("four", return_str->get_str());
+
+ }
+
+@@ -143,7 +143,7 @@ TEST_F(ListTest,_SubStrConstructorListTe
+ _String* str = new _String(",one,two,three");
+ _List list = _List((BaseRef)str, ',');
+ _String* return_string = (_String*)list[1];
+- EXPECT_STREQ("one", return_string->getStr());
++ EXPECT_STREQ("one", return_string->get_str());
+ }
+
+ TEST_F(ListTest,_DataConstructorListTest){
+@@ -152,7 +152,7 @@ TEST_F(ListTest,_DataConstructorListTest
+ _List list = _List((BaseRef)string);
+ _String* return_string = (_String*)list[0];
+
+- EXPECT_STREQ("one", return_string->getStr());
++ EXPECT_STREQ("one", return_string->get_str());
+
+ }
+
+@@ -161,7 +161,7 @@ TEST_F(ListTest,paranthesisTest){
+ _List str_list = createStrList();
+ _String* return_string = (_String*)str_list(4);
+
+- EXPECT_STREQ("four", return_string->getStr());
++ EXPECT_STREQ("four", return_string->get_str());
+ }
+
+ TEST_F(ListTest,EqualOpTest){
+@@ -169,7 +169,7 @@ TEST_F(ListTest,EqualOpTest){
+ _List str_list = createStrList();
+ _List list = str_list;
+ _String* return_string = (_String*)list[4];
+- EXPECT_STREQ("four", return_string->getStr());
++ EXPECT_STREQ("four", return_string->get_str());
+
+ }
+
+@@ -202,7 +202,7 @@ TEST_F(ListTest,AmpersandOpTest){
+ _List result_list = list & append_list;
+
+ _String* result_string = (_String*)result_list[0];
+- EXPECT_STREQ("one", result_string->getStr());
++ EXPECT_STREQ("one", result_string->get_str());
+
+
+ _List* l2 = new _List();
+@@ -220,7 +220,7 @@ TEST_F(ListTest,Ampersand2OpTest){
+
+ _String* result_string = (_String*)result_list[result_list.lLength-1];
+
+- EXPECT_STREQ("one",result_string->getStr());
++ EXPECT_STREQ("one",result_string->get_str());
+ }
+
+ TEST_F(ListTest,DoubleAmpersandOpTest){
+@@ -232,7 +232,7 @@ TEST_F(ListTest,DoubleAmpersandOpTest){
+
+ _String* result_string = (_String*)str_list[str_list.lLength-1];
+
+- EXPECT_STREQ("one",result_string->getStr());
++ EXPECT_STREQ("one",result_string->get_str());
+
+ }
+
+@@ -240,7 +240,7 @@ TEST_F(ListTest,DoubleAmpersand2OpTest){
+ _List str_list = createStrList();
+ str_list && "one";
+ _String* result_string = (_String*)str_list[str_list.lLength-1];
+- EXPECT_STREQ("one",result_string->getStr());
++ EXPECT_STREQ("one",result_string->get_str());
+ }
+
+ TEST_F(ListTest,DoubleLessOpTest){
+@@ -251,7 +251,7 @@ TEST_F(ListTest,DoubleLessOpTest){
+ str_list << str;
+
+ _String* result_string = (_String*)str_list[str_list.lLength-1];
+- EXPECT_STREQ("one", result_string->getStr());
++ EXPECT_STREQ("one", result_string->get_str());
+ }
+
+ TEST_F(ListTest,DoubleLess2OpTest){
+@@ -272,7 +272,7 @@ TEST_F(ListTest,DoubleLess2OpTest){
+ _List result_list = list;
+
+ _String* result_string = (_String*)result_list[5];
+- EXPECT_STREQ(expected_string->getStr(), result_string->getStr());
++ EXPECT_STREQ(expected_string->get_str(), result_string->get_str());
+
+ }
+
+@@ -283,7 +283,7 @@ TEST_F(ListTest,AppendNewInstanceTest){
+ str_list.AppendNewInstance(new _String("one"));
+ _String* result_string = (_String*)str_list[7];
+
+- EXPECT_STREQ("one", result_string->getStr());
++ EXPECT_STREQ("one", result_string->get_str());
+ }
+
+ TEST_F(ListTest,PlaceTest){
+@@ -294,7 +294,7 @@ TEST_F(ListTest,PlaceTest){
+ str_list.Place(new _String("one"));
+
+ _String* result_string = (_String*)str_list[7];
+- EXPECT_STREQ("one", result_string->getStr());
++ EXPECT_STREQ("one", result_string->get_str());
+ }
+
+ TEST_F(ListTest,InsertElementTest){
+@@ -302,7 +302,7 @@ TEST_F(ListTest,InsertElementTest){
+ _List str_list = createStrList();
+ str_list.InsertElement(new _String("one"),3,true);
+ _String* result_string = (_String*)str_list[3];
+- EXPECT_STREQ("one", result_string->getStr());
++ EXPECT_STREQ("one", result_string->get_str());
+ }
+
+ TEST_F(ListTest,getStrTest){
+@@ -312,7 +312,7 @@ TEST_F(ListTest,getStrTest){
+ _String* str = new _String("{zero, one, two, three, four, five, six}");
+ _String* result_string = (_String*)str_list.toStr();
+
+- EXPECT_STREQ(str->getStr(), result_string->getStr());
++ EXPECT_STREQ(str->get_str(), result_string->get_str());
+
+ }
+
+@@ -333,7 +333,7 @@ TEST_F(ListTest,bumpNInstTest){
+ str_list.bumpNInst();
+
+ _String* result_string = (_String*)str_list[3];
+- EXPECT_STREQ("three", result_string->getStr());
++ EXPECT_STREQ("three", result_string->get_str());
+ }
+
+ TEST_F(ListTest,FindStringTest){
+@@ -362,7 +362,7 @@ TEST_F(ListTest,JoinTest){
+ _String* spacer = new _String(";");
+ _List* list = new _List((BaseRef)str, ',');
+ _String* return_string = (_String*)list->Join((BaseRef)spacer);
+- EXPECT_STREQ("one;two;three", return_string->getStr());
++ EXPECT_STREQ("one;two;three", return_string->get_str());
+ }
+
+ TEST_F(ListTest,BinaryFindTest){
+@@ -385,7 +385,7 @@ TEST_F(ListTest,BinaryInsertTest){
+ str_list.BinaryInsert((BaseRef)new _String("one"));
+
+ _String* result_string = (_String*)str_list[3];
+- EXPECT_STREQ("three", result_string->getStr());
++ EXPECT_STREQ("three", result_string->get_str());
+ }
+
+ TEST_F(ListTest,CompareTest){
+@@ -420,7 +420,7 @@ TEST_F(ListTest,DeleteTest){
+ _List str_list = createStrList();
+ str_list.Delete(0);
+ _String* return_string = (_String*)str_list[1];
+- EXPECT_STREQ("two", return_string->getStr());
++ EXPECT_STREQ("two", return_string->get_str());
+ }
+
+ TEST_F(ListTest,DeleteListTest){
+@@ -441,11 +441,11 @@ TEST_F(ListTest,ReplaceTest){
+
+ str_list.Replace(1, new _String("help"), false);
+ _String* return_string = (_String*)str_list[1];
+- EXPECT_STREQ("help", return_string->getStr());
++ EXPECT_STREQ("help", return_string->get_str());
+
+ str_list.Replace(1, new _String("two"), false);
+ _String* return_string2 = (_String*)str_list[1];
+- EXPECT_STREQ("two", return_string2->getStr());
++ EXPECT_STREQ("two", return_string2->get_str());
+ }
+
+
+@@ -464,7 +464,7 @@ TEST_F(ListTest,IntersectTest){
+ l3.Intersect(l1, l2, &idx, &idx2);
+
+ _String* return_string = (_String*)str_list[1];
+- EXPECT_STREQ("one",return_string->getStr());
++ EXPECT_STREQ("one",return_string->get_str());
+
+ }
+
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ use_debian_sqlite.patch
drop_profiling_option.patch
remove_unneeded_test.patch
# msse_option_only_if_available.patch
+gcc9.patch
=====================================
debian/patches/use_debian_sqlite.patch
=====================================
@@ -20,7 +20,7 @@ Description: Use Debian packaged sqlite3
set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")
#-------------------------------------------------------------------------------
-@@ -264,6 +263,36 @@ if(${CURL_FOUND} AND NOT APPLE)
+@@ -265,6 +264,36 @@ if(${CURL_FOUND} AND NOT APPLE)
endif(${CURL_FOUND} AND NOT APPLE)
#-------------------------------------------------------------------------------
@@ -57,7 +57,7 @@ Description: Use Debian packaged sqlite3
# gtest dependency
#-------------------------------------------------------------------------------
add_subdirectory(contrib/gtest-1.7.0)
-@@ -305,11 +334,6 @@ set_property(
+@@ -306,11 +335,6 @@ set_property(
)
set_property(
@@ -69,7 +69,7 @@ Description: Use Debian packaged sqlite3
SOURCE src/core/calcnode2.cpp
APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"
)
-@@ -329,7 +353,6 @@ include_directories(
+@@ -330,7 +354,6 @@ include_directories(
src/core/include
src/contrib
src/lib/Link src/new/include
View it on GitLab: https://salsa.debian.org/med-team/hyphy/compare/df335440535562f7c62290cfdf726ced74abcdd8...6176567316bb409c1d39967a98343e6d9b7c611d
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/compare/df335440535562f7c62290cfdf726ced74abcdd8...6176567316bb409c1d39967a98343e6d9b7c611d
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