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

+Author: Andreas Tille <tille@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