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veg / hyphy

HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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Compile Error During Make on Windows 10 #781

Closed rentiandong closed 6 years ago

rentiandong commented 6 years ago

Hi, I am following the installation instructions on http://hyphy.org/installation/. I have installed make from https://www.gnu.org/software/make/.

Since I am on windows, I used -G unix Makefiles so that a makefile is produced. All other steps were identical to that from the website. When I get to the command make -j MP, a large amount of compile errors show up.

Here are all the commands I used and their outputs. I apologize in advance for the large volume, and any help is greatly appreciated!

C:\Users\Rentian Dong\Desktop>git clone https://github.com/veg/hyphy.git
Cloning into 'hyphy'...
remote: Counting objects: 22871, done.
remote: Compressing objects: 100% (191/191), done.
remote: Total 22871 (delta 113), reused 111 (delta 56), pack-reused 22620
Receiving objects: 100% (22871/22871), 70.79 MiB | 7.26 MiB/s, done.
Resolving deltas: 100% (16700/16700), done.
Checking out files: 100% (1073/1073), done.

C:\Users\Rentian Dong\Desktop>git pull origin master
fatal: Not a git repository (or any of the parent directories): .git

C:\Users\Rentian Dong\Desktop>cd hyphy

C:\Users\Rentian Dong\Desktop\hyphy>git pull origin master
From https://github.com/veg/hyphy
 * branch              master     -> FETCH_HEAD
Already up to date.

C:\Users\Rentian Dong\Desktop\hyphy>cmake -G "Unix Makefiles" .
-- The C compiler identification is GNU 5.2.0
-- The CXX compiler identification is GNU 5.2.0
-- Check for working C compiler: C:/Program Files/Haskell Platform/8.0.1/mingw/bin/gcc.exe
-- Check for working C compiler: C:/Program Files/Haskell Platform/8.0.1/mingw/bin/gcc.exe -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: C:/Program Files/Haskell Platform/8.0.1/mingw/bin/c++.exe
-- Check for working CXX compiler: C:/Program Files/Haskell Platform/8.0.1/mingw/bin/c++.exe -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
Set compiler flags to -fsigned-char -O3 -std=gnu++14 -march=corei7-avx -mtune=corei7-avx
-- Found OpenMP_C: -fopenmp (found version "4.0")
-- Found OpenMP_CXX: -fopenmp (found version "4.0")
-- Found OpenMP: TRUE (found version "4.0")
-- Could NOT find CURL (missing: CURL_INCLUDE_DIR)
-- Found PythonInterp: C:/Users/Rentian Dong/AppData/Local/Programs/Python/Python36/python.exe (found version "3.6.3")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Could NOT find OpenCL (missing: OPENCL_INCLUDE_DIR)
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
-- Configuring done
-- Generating done
-- Build files have been written to: C:/Users/Rentian Dong/Desktop/hyphy

C:\Users\Rentian Dong\Desktop\hyphy>make -j MP
makefile:255: warning: overriding commands for target `GTEST'
makefile:242: warning: ignoring old commands for target `GTEST'
makefile:260: warning: overriding commands for target `GTEST/fast'
makefile:247: warning: ignoring old commands for target `GTEST/fast'
Scanning dependencies of target HYPHYMP
[  3%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.obj
[  6%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.obj
[  6%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllist.cpp.obj
[  9%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistx.cpp.obj
[  9%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistxl.cpp.obj
[ 12%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistxl_iterator.cpp.obj
[ 15%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/baseobj.cpp.obj
[ 15%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlan.cpp.obj
[ 18%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlan2.cpp.obj
[ 18%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlanhelpers.cpp.obj
[ 21%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlanruntime.cpp.obj
[ 25%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/calcnode.cpp.obj
[ 25%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/calcnode2.cpp.obj
[ 28%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/category.cpp.obj
[ 31%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/constant.cpp.obj
[ 31%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/error.cpp.obj
[ 34%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/fisher_exact.cpp.obj
[ 34%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/formula.cpp.obj[ 37%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/fstring.cpp.obj

[ 40%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/global_object_lists.cpp.obj
[ 40%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/hbl_env.cpp.obj
[ 43%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/likefunc.cpp.obj
[ 43%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/likefunc2.cpp.obj[ 46%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/likefuncocl.cpp.obj

[ 50%] [ 50%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/matrix.cpp.obj[ 53%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/list.cpp.obj
Building CXX object CMakeFiles/HYPHYMP.dir/src/core/mathobj.cpp.obj

[ 56%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/operation.cpp.obj
[ 56%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/nexus.cpp.obj
[ 59%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/parser.cpp.obj
[ 59%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/parser2.cpp.obj
[ 62%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/polynoml.cpp.obj
[ 65%] [ 65%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/sequence.cpp.obj
Building CXX object CMakeFiles/HYPHYMP.dir/src/core/regex.cpp.obj
[ 68%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/simplelist.cpp.obj
[ 68%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/site.cpp.obj
[ 71%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/stack.cpp.obj
[ 75%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/string_file_wrapper.cpp.obj
[ 78%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/time_difference.cpp.obj
[ 81%] [ 81%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/variable.cpp.obj
[ 81%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/trie.cpp.objBuilding CXX object CMakeFiles/HYPHYMP.dir/src/core/strings.cpp.obj[ 84%]

[ 84%] Building CXX object CMakeFiles/HYPHYMP.dir/src/new/bayesgraph.cpp.obj
Building CXX object CMakeFiles/HYPHYMP.dir/src/core/variablecontainer.cpp.obj
[ 87%] Building CXX object CMakeFiles/HYPHYMP.dir/src/new/bayesgraph2.cpp.obj
[ 87%] Building CXX object CMakeFiles/HYPHYMP.dir/src/new/bgm.cpp.obj
[ 90%] Building CXX object CMakeFiles/HYPHYMP.dir/src/new/bgm2.cpp.obj
[ 93%] Building CXX object CMakeFiles/HYPHYMP.dir/src/new/scfg.cpp.obj
[ 93%] Building C object CMakeFiles/HYPHYMP.dir/contrib/SQLite-3.8.2/sqlite3.c.obj
[ 96%] Building CXX object CMakeFiles/HYPHYMP.dir/src/utils/hyphyunixutils.cpp.obj
[ 96%] Building CXX object CMakeFiles/HYPHYMP.dir/src/mains/unix.cpp.obj
dow.h: No such file or directory
coIn file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/mathobj.h:46:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/constant.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variable.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variablecontainer.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/_hyExecutionContext.cpp:41:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/avllist.h:43:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllist.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/category.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/likefunc.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/alignment.h:41,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/alignment.cpp:43:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/avllistxl.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/avllistxl_iterator.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllistxl_iterator.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/site.cpp:68:25: fatal error: HYDataPanel.h: No such file or directory
^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/avllistx.h:43:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllistx.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hbl_env.h:38,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/hbl_env.cpp:38:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/calcnode.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode2.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/batchlanruntime.cpp:44:0:
C:/Users/Rentian Dong/Desktop/hyphy/src/new/include/bayesgraph.h:45:29: fatal error: HYConsoleWindow.h: No such file or directory
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/calcnode.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:43:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/sequence.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/site.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/nexus.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/strings.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/avllistxl.h:44:0,
           ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser2.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/batchlan2.cpp:46:0:
C:/Users/Rentian Dong/Desktop/hyphy/src/new/include/bayesgraph.h:45:29: fatal error: HYConsoleWindow.h: No such file or directory
mmake[3]: C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllist.cpp: In member function 'virtual BaseObj* _AVLList::toStr(long unsigned int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllist.cpp:430:48: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
            (*str) << _String((long)Retrieve (cn));
                                                ^
*** [CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.obj] Error 1C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp: In member function 'virtual void _CalcNode::ReplaceModel(_String&, _VariableContainer*)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:488:85: error: cast from '_CalcNode*' to 'long int' loses precision [-fpermissive]
     long index_in_parent = parent_tree_object->flatCLeaves._SimpleList::Find ((long)this);
                                                                                     ^

In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/polynoml.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/polynoml.cpp:43:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
make[3]: c*** Waiting for unfinished jobs....o
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/mathobj.h:46:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/constant.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variable.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variablecontainer.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/variablecontainer.cpp:41:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
make[3]: C:/Users/Rentian Dong/Desktop/hyphy/src/core/variablecontainer.cpp: In member function 'void _VariableContainer::ScanModelBasedVariables(_String&, _AVLListXL*)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/variablecontainer.cpp:301:82: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
                     varCache->Insert ((BaseRef)theModel, (long)mVars.makeDynamic(),false);
                                                                                  ^
*** [CMakeFiles/HYPHYMP.dir/src/core/alignment.cppIn file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/mathobj.h:46:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/fstring.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/fstring.cpp:41:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/string_file_wrapper.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/string_file_wrapper.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
cC:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp: In member function '_Formula* _Formula::Differentiate(_String, bool, bool)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:243:27: error: cast from '_Formula*' to 'long int' loses precision [-fpermissive]
             dydx << (long)dYdX;
                           ^
pIn file included from C:/Users/Rentian Dong/Desktop/hyphy/src/new/include/scfg.h:61:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/new/scfg.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
mIn file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/sequence.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/site.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/global_object_lists.h:38,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp:39:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/new/bayesgraph2.cpp:41:0:
C:/Users/Rentian Dong/Desktop/hyphy/src/new/include/bayesgraph.h:45:29: fatal error: HYConsoleWindow.h: No such file or directory
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/baseobj.cpp:43:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/matrix.cpp:64:29: fatal error: HYConsoleWindow.h: No such file or directory
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/mathobj.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/list.cpp:40:0:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/likefunc.cpp:98:37: fatal error: HYTreePanel.h: No such file or directory
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp: In function 'int re_match_2(re_pattern_buffer*, const char*, int, const char*, int, int, re_registers*, int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:3877:52: error: cast from 'const char*' to 'long int' loses precision [-fpermissive]
                             if ((long) old_regend[r] >= (long) regstart[r])
                                                    ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/new/bayesgraph.cpp:41:0:
C:/Users/Rentian Dong/Desktop/hyphy/src/new/include/bayesgraph.h:45:29: fatal error: HYConsoleWindow.h: No such file or directory
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/category.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/likefunc.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/likefunc2.cpp:44:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllistxl.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
cC:/Users/Rentian Dong/Desktop/hyphy/src/core/category.cpp: In member function 'void _CategoryVariable::Construct(_List&, _VariableContainer*)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/category.cpp:263:149: error: cast from '_SimpleList*' to 'long int' loses precision [-fpermissive]
                                         f = variableDependanceAllocations.Insert ((BaseRef)probVars.lData[v], (long)(new _SimpleList (intervals,0,0)),false);
                                                                                                                                                     ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/batchlan.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/batchlanhelpers.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/fisher_exact.cpp:21:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/simplelist.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/sequence.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/sequence.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
           ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/trie.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/trie.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/simplelist.cpp: In member function 'virtual long int _SimpleList::Compare(const BaseObj*, long int) const':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/simplelist.cpp:341:24: error: cast from 'const BaseObj*' to 'long int' loses precision [-fpermissive]
     long    v1 = (long)i,
                        ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:495:79: error: cast from '_CalcNode*' to 'long int' loses precision [-fpermissive]
       index_in_parent = parent_tree_object->flatTree._SimpleList::Find ((long)this);
                                                                               ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/classes.h:209:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:49,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/calcnode.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode2.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp: In instantiation of 'void node_iterator<node_data>::push_history_item(_SimpleList*) [with node_data = long int]':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:87:11:   required from 'node<node_data>* node_iterator<node_data>::Next(_SimpleList*) [with node_data = long int]'
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode2.cpp:2546:60:   required from here
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:73:15: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
     (*history)<< (long)this->iterator_state;
               ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp: In member function 'virtual bool _TreeTopology::MainTreeConstructor(_String&, bool, _AssociativeList*)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:1540:34: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
                 nodeStack<<(long)currentNode;
                                  ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/hy_strings.h:45:0,
                   ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/mathobj.h:46:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/constant.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/constant.cpp:48:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/mathobj.h:46:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/stack.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/stack.cpp:40:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/category.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/likefunc.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:44:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
.obj] Error 1c
C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllistxl.cpp: In member function 'virtual long int _AVLListXL::UpdateValue(BaseRef, BaseRef, bool, bool)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/avllistxl.cpp:121:51: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
         Insert (copy_key?b->makeDynamic():b,(long)d, do_copy);
                                                   ^
make[3]: cC:/Users/Rentian Dong/Desktop/hyphy/src/new/scfg.cpp: In member function 'void Scfg::ProcessAFormula(_FString*, _List&, _SimpleList&, _String&)':
C:/Users/Rentian Dong/Desktop/hyphy/src/new/scfg.cpp:575:33: error: cast from '_Formula*' to 'long int' loses precision [-fpermissive]
         parsedFormulas << (long)aFormula;
                                 ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp: In function 'bool hyphy_global_objects::UnregisterChangeListenerForDataFilter(long int, BaseRef)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp:235:76: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
           long listener_index = current_listeners->_SimpleList::Find((long)listener);
                                                                            ^
cC:/Users/Rentian Dong/Desktop/hyphy/src/core/baseobj.cpp: In function 'bool GlobalStartup()':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/baseobj.cpp:229:39: error: 'getpid' was not declared in this scope
     seed_init               += getpid();
                                       ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:3877:74: error: cast from 'const char*' to 'long int' loses precision [-fpermissive]
                             if ((long) old_regend[r] >= (long) regstart[r])
                                                                          ^
ooC:/Users/Rentian Dong/Desktop/hyphy/src/core/category.cpp:484:148: error: cast from '_SimpleList*' to 'long int' loses precision [-fpermissive]
                                     f = variableDependanceAllocations.Insert ((BaseRef)densityVars.lData[v], (long)(new _SimpleList (intervals,0,0)),false);
                                                                                                                                                    ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/mathobj.h:46:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/constant.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variable.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/operation.cpp:41:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/mathobj.h:46:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/constant.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variable.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/variable.cpp:41:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:1547:30: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
             nodeStack<<(long)currentNode;
                              ^
oC:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:251:27: error: cast from '_Formula*' to 'long int' loses precision [-fpermissive]
             dydx << (long)dYdX;
                           ^
ipcIn file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/classes.h:209:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/formula.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variable.h:48,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/variablecontainer.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/matrix.h:45,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/fstring.cpp:43:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp: In instantiation of 'void node_iterator<node_data>::push_history_item(_SimpleList*) [with node_data = long int]':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:87:11:   required from 'node<node_data>* node_iterator<node_data>::Next(_SimpleList*) [with node_data = long int]'
C:/Users/Rentian Dong/Desktop/hyphy/src/core/fstring.cpp:503:44:   required from here
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:73:15: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
     (*history)<< (long)this->iterator_state;
               ^
*** [CMakeFiles/HYPHYMP.dir/src/core/avllist.cpp.obj] Error 1C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:2434:63: error: cast from 'fail_stack_elt_t {aka const unsigned char*}' to 'long unsigned int' loses precision [-fpermissive]
 #define POP_FAILURE_ITEM() fail_stack.stack[--fail_stack.avail]
                                                               ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:2599:30: note: in expansion of macro 'POP_FAILURE_ITEM'
   high_reg = (unsigned long) POP_FAILURE_ITEM ();               \
                              ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:4195:13: note: in expansion of macro 'POP_FAILURE_POINT'
             POP_FAILURE_POINT (sdummy, pdummy,
             ^
mmC:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:1578:34: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
                 nodeStack<<(long)currentNode;
                                  ^
mlC:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp: In member function 'bool _Formula::ConvertToSimple(_SimpleList&)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:1703:40: error: cast from '_Parameter (*)(_Parameter) {aka double (*)(double)}' to 'long int' loses precision [-fpermissive]
                 thisOp->opCode = (long)MinusNumber;
                                        ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/variable.cpp: In member function 'void _Variable::SetValue(_PMathObj, bool)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/variable.cpp:401:96: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             variablePtrs.lData[theIndex] = (long)(((_TheTree*)theP)->makeDynamicCopy(GetName()));
                                                                                                ^
iooC:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp: In function 'bool hyphy_global_objects::RegisterChangeListenerForDataFilter(long int, BaseRef)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp:260:64: error: cast from '_List*' to 'long int' loses precision [-fpermissive]
           _data_filter_listeners.Insert ((BaseRef)index, (long)current_listeners, false, false);
                                                                ^
oC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp: In function 'void SetupOperationLists()':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:817:42: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<< (long)AndNumbers;
                                          ^

pmake[3]: m*** [CMakeFiles/HYPHYMP.dir/src/C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp: In member function 'void _Formula::ConvertFromSimple(_SimpleList&)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:1735:48: error: cast from '_Parameter (*)(_Parameter) {aka double (*)(double)}' to 'long int' loses precision [-fpermissive]
             } else if (thisOp->opCode == (long)MinusNumber) {
                                                ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp: In member function 'void _TheTree::SetUp()':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:2418:42: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
           flatLeaves << (long)ti.GetNode();
                                          ^
lmmC:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp:263:56: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
         if (current_listeners->_SimpleList::Find((long)listener) < 0L) {
                                                        ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:822:42: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<< (long)MultNumbers;
                                          ^
pC:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:2434:63: error: cast from 'fail_stack_elt_t {aka const unsigned char*}' to 'long unsigned int' loses precision [-fpermissive]
 #define POP_FAILURE_ITEM() fail_stack.stack[--fail_stack.avail]
                                                               ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:2602:29: note: in expansion of macro 'POP_FAILURE_ITEM'
   low_reg = (unsigned long) POP_FAILURE_ITEM ();                \
                             ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:4195:13: note: in expansion of macro 'POP_FAILURE_POINT'
             POP_FAILURE_POINT (sdummy, pdummy,
             ^
pipacC:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:1738:45: error: cast from '_Parameter (*)(Ptr, _Parameter) {aka double (*)(char*, double)}' to 'long int' loses precision [-fpermissive]
                 if (thisOp->opCode == (long)FastMxAccess) {
                                             ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:2419:57: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
           flatParents << (long)ti.GetNode()->get_parent();
                                                         ^
appC:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp: In function 'long int hyphy_global_objects::StoreDataFilter(const _String&, _DataSetFilter*, bool)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/global_object_lists.cpp:319:73: error: cast from '_DataSetFilter*' to 'long int' loses precision [-fpermissive]
         exists_already = _data_filters.Insert (new _String(name), (long)object, false, false);
                                                                         ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:827:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)AddNumbers;
                                         ^
iilitore/avllistx.cppC:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:2434:63: error: cast from 'fail_stack_elt_t {aka const unsigned char*}' to 'long unsigned int' loses precision [-fpermissive]
 #define POP_FAILURE_ITEM() fail_stack.stack[--fail_stack.avail]
                                                               ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:2599:30: note: in expansion of macro 'POP_FAILURE_ITEM'
   high_reg = (unsigned long) POP_FAILURE_ITEM ();               \
                              ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:4417:13: note: in expansion of macro 'POP_FAILURE_POINT'
             POP_FAILURE_POINT (d, p,
             ^
iillaC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:832:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)SubNumbers;
                                         ^
liC:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:1741:47: error: cast from 'void (*)(Ptr, _Parameter, _Parameter) {aka void (*)(char*, double, double)}' to 'long int' loses precision [-fpermissive]
                   if (thisOp->opCode == (long)FastMxWrite) {
                                               ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:2422:42: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
             flatNodes<< (long)ti.GetNode();
                                          ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp: In member function 'bool _Formula::HasChangedSimple(_SimpleList&)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:1991:42: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
             if (thisOp->opCode == (long) RandomNumber) {
                                          ^
tC:/Users/Rentian Dong/Desktop/hyphy/src/core/regex.cpp:2434:63: error: cast from 'fail_stack_elt_t {  ^
llaatC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:837:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)DivNumbers;
                                         ^
ao.obj] Error 1C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp: In member function 'void _Formula::ConvertToTree(bool)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:2253:34: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
                 nodeStack<<(long)leafNode;
                                  ^

amaketnC:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:2424:64: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
             flatINodeParents << (long)ti.GetNode()->get_parent();
                                                                ^
iC:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:2273:34: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
                 nodeStack<<(long)operationNode;
                                  ^
atttiC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:842:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)LessThan;
                                         ^
[3]: C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp: In member function 'virtual _AssociativeList* _TreeTopology::FindCOT(_PMathObj)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:2865:28: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
       listOfNodes << (long)iterator;
                            ^
iIn file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/classes.h:209:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/formula.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:43:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp: In instantiation of 'void node_iterator<node_data>::push_history_item(_SimpleList*) [with node_data = long int]':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:87:11:   required from 'node<node_data>* node_iterator<node_data>::Next(_SimpleList*) [with node_data = long int]'
C:/Users/Rentian Dong/Desktop/hyphy/src/core/formula.cpp:1935:43:   required from here
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:73:15: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
     (*history)<< (long)this->iterator_state;
               ^
ioiC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:847:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)LessThanE;
                                         ^
 ot*** [CMakeFiles/HYPHYMP.dir/src/core/avliioonC:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp: In member function 'char _TreeTopology::internalTreeCompare(node<long int>*, node<long int>*, _SimpleList*, char, long int, node<long int>*, const _TreeTopology*, bool) const':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:3434:42: error: cast from '_SimpleList*' to 'long int' loses precision [-fpermissive]
                 dummy->in_object = (long)newLeaves;
                                          ^
oC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:852:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)EqualNumbers;
                                         ^
tneoonn nC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:857:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)GreaterThan;
                                         ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp: In member function 'const _String _TheTree::FindMaxCommonSubTree(const _TheTree*, long int&, _List*) const':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:3531:31: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
                 ldx1 << (long)iterator;
                               ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:862:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)GreaterThanE;
                                         ^
 rtm  t listxl.cpp.obj] Error 1nn ittetC:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:3538:31: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
                 ldx2 << (long)iterator;
                               ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:867:41: error: cast from '_Parameter (*)(_Parameter) {aka double (*)(double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)AbsNumber;
                                         ^

 tneereC:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:3569:42: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
                     matchedTops << (long)ln1;
                                          ^
C:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:931:41: error: cast from '_Parameter (*)(_Parameter) {aka double (*)(double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)ExpNumbers;
                                         ^
etemake[3]: rarrmrC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:984:41: error: cast from '_Parameter (*)(_Parameter) {aka double (*)(double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)LogNumbers;
                                         ^
re*** [CMakeFiles/HYPHYMP.dir/src/core/avllistxl_iterator.cpp.obj] Error 1rmtmmimC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:989:41: error: cast from '_Parameter (*)(Ptr, _Parameter) {aka double (*)(char*, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)FastMxAccess;
                                         ^
m
ieiiniC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:994:41: error: cast from 'void (*)(Ptr, _Parameter, _Parameter) {aka void (*)(char*, double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)FastMxWrite;
                                         ^
immake[3]: i**nnanC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:1001:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)MaxNumbers;
                                         ^
nnnd*aattC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:1008:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)MinNumbers;
                                         ^
aaa [CMakeFiles/HYPHYMP.dir/src/core/baseobj.cpp.obj] Error 1eetC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:1020:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)RandomNumber;
                                         ^
tC:/Users/Rentian Dong/Desktop/hyphy/src/core/parser.cpp:1075:41: error: cast from '_Parameter (*)(_Parameter, _Parameter) {aka double (*)(double, double)}' to 'long int' loses precision [-fpermissive]
         simpleOperationFunctions<<(long)Power;
                                         ^
.ta
detemake[3]: d
etd.deC:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp: In member function 'node<long int>* _TreeTopology::prepTree4Comparison(_List&, _SimpleList&, node<long int>*) const':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:7094:37: error: cast from '_SimpleList*' to 'long int' loses precision [-fpermissive]
         iterator->in_object = (long)descendants;
                                     ^
*** [CMakeFiles/HYPHYMP.dir/src/core/batchlanhelpers.cpp.obj] Error 1

.deIn file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/classes.h:209:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:49,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/calcnode.h:43,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:43:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp: In instantiation of 'void node_iterator<node_data>::push_history_item(_SimpleList*) [with node_data = long int]':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:87:11:   required from 'node<node_data>* node_iterator<node_data>::Next(_SimpleList*) [with node_data = long int]'
C:/Users/Rentian Dong/Desktop/hyphy/src/core/calcnode.cpp:1341:59:   required from here
C:/Users/Rentian Dong/Desktop/hyphy/src/core/classes.cp:73:15: error: cast from 'node<long int>*' to 'long int' loses precision [-fpermissive]
     (*history)<< (long)this->iterator_state;
               ^
..dmake[3]: d

.
.*** [CMakeFiles/HYPHYMP

..dir/src/core/batc
hlan.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/batchlanruntime.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/batchlan2.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/calcnode2.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/category.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/constant.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/error.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/fisher_exact.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/formula.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/fstring.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/calcnode.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/global_object_lists.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/hbl_env.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/likefunc.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/likefunc2.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/list.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/mathobj.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/matrix.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/nexus.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/operation.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/parser.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/parser2.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/polynoml.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/regex.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/sequence.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/simplelist.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/site.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/stack.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/string_file_wrapper.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/strings.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/trie.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/variable.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/core/variablecontainer.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/new/bayesgraph.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/new/bayesgraph2.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/new/scfg.cpp.obj] Error 1
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/utils/hyphyunixutils.cpp.obj] Error 1
In file included from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/parser.h:44:0,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/batchlan.h:44,
                 from C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp:32:
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h: In member function 'virtual long int _List::FindPointer(BaseRef, long int)':
C:/Users/Rentian Dong/Desktop/hyphy/src/core/include/list.h:273:44: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
             return _SimpleList::Find((long)b, startat);
                                            ^
C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp: In function '_String getLibraryPath()':
C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp:245:21: error: aggregate 'getLibraryPath()::stat sb' has incomplete type and cannot be defined
         struct stat sb;
                     ^
C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp:247:44: error: invalid use of incomplete type 'struct getLibraryPath()::stat'
         if (stat((const char*)tryLocal, &sb) == 0 && S_ISDIR(sb.st_mode)) {
                                            ^
C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp:245:16: note: forward declaration of 'struct getLibraryPath()::stat'
         struct stat sb;
                ^
C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp:247:72: error: 'S_ISDIR' was not declared in this scope
         if (stat((const char*)tryLocal, &sb) == 0 && S_ISDIR(sb.st_mode)) {
                                                                        ^
C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp: In function 'int main(int, char**)':
C:/Users/Rentian Dong/Desktop/hyphy/src/mains/unix.cpp:874:102: error: cast from 'BaseRef {aka BaseObj*}' to 'long int' loses precision [-fpermissive]
                     ex.stdinRedirect->Insert (new _String(buf), (long)positional_arguments.GetItem (i), true);
                                                                                                      ^
make[3]: *** [CMakeFiles/HYPHYMP.dir/src/mains/unix.cpp.obj] Error 1
make[2]: *** [CMakeFiles/HYPHYMP.dir/all] Error 2
make[1]: *** [CMakeFiles/MP.dir/rule] Error 2
make: *** [MP] Error 2
stevenweaver commented 6 years ago

Dear @r2dong,

We do not currently support building on Windows. We are planning on investigating how to do this soon. Sincerest apologies for the delay in response.

Best, Steven