Visual Studio failed with exit status 2

[scikit-tda]

Visual Studio failed with exit status 2

[ctralie]

Hello Jacob,
Sorry for the trouble, and thank you for the detailed bug report!

Unfortunately, ripser.py doesn't support the Visual Studio compiler. We actually have a prebuilt binary on pypi that was built with mingw. I believe this is the download link for the mingw runtimes
https://sourceforge.net/projects/mingw-w64/
Installing it alongside VS shouldn't be a problem.

So try installing the mingw runtimes, and then try ``pip install ripser'' again (you'll have to elaborate on the --no-cache-dir if that happens again...I haven't heard of that before. You're not downloading the source, are you)?)

Let me know if that works, and sorry again for the trouble
-Chris

[JacobPfau]

Ok thanks for the pointer. As I understand it, to use a non-default compiler you have to manually download and then build using --compiler=mingw32. I tried this as shown below, but I received a new error message.

C:\Users\jacob\ripser-0.3.0>python setup.py build --compiler=mingw32
running build
running build_py
running build_ext
building 'pyRipser' extension
C:\Program Files\mingw-w64\x86_64-8.1.0-posix-seh-rt_v6-rev0\mingw64\bin\gcc.exe -mdll -O -Wall -DMS_WIN64 -DUSE_COEFFICIENTS=1 -DNDEBUG=1 -DASSEMBLE_REDUCTION_MATRIX=1 -I.\ripser -IC:\Users\jacob\Anaconda3\include -IC:\Users\jacob\Anaconda3\include -IC:\Users\jacob\Anaconda3\lib\site-packages\numpy\core\include -c ripser/pyRipser.cpp -o build\temp.win-amd64-3.7\Release\ripser\pyripser.o -std=c++11 -Ofast -D_hypot=hypot
In file included from C:\Users\jacob\Anaconda3\lib\site-packages\numpy\core\include/numpy/ndarraytypes.h:1821,
                 from C:\Users\jacob\Anaconda3\lib\site-packages\numpy\core\include/numpy/ndarrayobject.h:18,
                 from C:\Users\jacob\Anaconda3\lib\site-packages\numpy\core\include/numpy/arrayobject.h:4,
                 from ripser/pyRipser.cpp:619:
C:\Users\jacob\Anaconda3\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h:13:79: note: #pragma message: C:\Users\jacob\Anaconda3\lib\site-packages\numpy\core\include/numpy/npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
                          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION")
                                                                               ^
ripser/pyRipser.cpp: In function 'PyTypeObject* __Pyx_ImportType(const char*, const char*, size_t, int)':
ripser/pyRipser.cpp:8275:13: warning: unknown conversion type character 'z' in format [-Wformat=]
             "%s.%s size changed, may indicate binary incompatibility. Expected %zd, got %zd",
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ripser/pyRipser.cpp:8275:13: warning: unknown conversion type character 'z' in format [-Wformat=]
ripser/pyRipser.cpp:8275:13: warning: too many arguments for format [-Wformat-extra-args]
In file included from ripser/pyRipser.cpp:626:
ripser/ripser.cpp: In instantiation of 'void ripser<DistanceMatrix>::compute_pairs(std::vector<std::pair<float, long long int> >&, hash_map<long long int, long long int>&, index_t) [with DistanceMatrix = compressed_distance_matrix<(compressed_matrix_layout)0>; index_t = long long int]':
ripser/ripser.cpp:800:5:   required from 'void ripser<DistanceMatrix>::compute_barcodes() [with DistanceMatrix = compressed_distance_matrix<(compressed_matrix_layout)0>]'
ripser/ripser.cpp:1031:22:   required from here
ripser/ripser.cpp:651:58: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'index_t' {aka 'long long int'} [-Wsign-compare]
    bool might_be_apparent_pair = (index_column_to_reduce == index_column_to_add);
                                  ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
ripser/ripser.cpp: In instantiation of 'void ripser<DistanceMatrix>::compute_pairs(std::vector<std::pair<float, long long int> >&, hash_map<long long int, long long int>&, index_t) [with DistanceMatrix = sparse_distance_matrix; index_t = long long int]':
ripser/ripser.cpp:800:5:   required from 'void ripser<DistanceMatrix>::compute_barcodes() [with DistanceMatrix = sparse_distance_matrix]'
ripser/ripser.cpp:1036:22:   required from here
ripser/ripser.cpp:651:58: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'index_t' {aka 'long long int'} [-Wsign-compare]
writing build\temp.win-amd64-3.7\Release\ripser\pyRipser.cp37-win_amd64.def
C:\Program Files\mingw-w64\x86_64-8.1.0-posix-seh-rt_v6-rev0\mingw64\bin\g++.exe -shared -s build\temp.win-amd64-3.7\Release\ripser\pyripser.o build\temp.win-amd64-3.7\Release\ripser\pyRipser.cp37-win_amd64.def -LC:\Users\jacob\Anaconda3\libs -LC:\Users\jacob\Anaconda3\PCbuild\amd64 -lpython37 -lmsvcr140 -o build\lib.win-amd64-3.7\pyRipser.cp37-win_amd64.pyd
C:/Program Files/mingw-w64/x86_64-8.1.0-posix-seh-rt_v6-rev0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0/../../../../x86_64-w64-mingw32/bin/ld.exe: cannot find -lmsvcr140
collect2.exe: error: ld returned 1 exit status
error: command 'C:\\Program Files\\mingw-w64\\x86_64-8.1.0-posix-seh-rt_v6-rev0\\mingw64\\bin\\g++.exe' failed with exit status 1

[sauln]

Have you tried installing without the flag? Once MinGW is installed, please try just the command

pip install ripser

[JacobPfau]

Yes I've tried that. I may be misunderstanding things, but I believe installing MinGW doesn't change the default compiler used by pip. I still get the same error message I did the first time.

I've also tried using MinGW by the command
pip install --global-option build_ext --global-option --compiler=mingw32 ripser

[sauln]

My apologies for the trouble, thanks for bearing with us. Windows is a weakness of mine.

I think if you add MinGW to your path, it might fix the problem. That was the solution in #46.

[JacobPfau]

That error came after adding MinGW to my path i.e. C:\Program Files\mingw-w64\x86_64-8.1.0-posix-seh-rt_v6-rev0\mingw64\bin;

If I do not add MinGW to my path I get a different error. See below. Thanks for bearing with me too, this seems to be more of a compiler issue on my end rather than a ripser issue. Perhaps the guy in the other thread installed a different version of MinGW? I'll take a look.

(base) C:\Users\jacob>pip install --global-option build_ext --global-option --compiler=mingw32 ripser
c:\users\jacob\anaconda3\lib\site-packages\pip\_internal\commands\install.py:211: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
  cmdoptions.check_install_build_global(options)
Collecting ripser
  Using cached https://files.pythonhosted.org/packages/20/59/302dab2f1be85f32c57bdf8d4595d0437db76131b13504025abfc8373b03/ripser-0.3.0.tar.gz
Requirement already satisfied: Cython in c:\users\jacob\anaconda3\lib\site-packages (from ripser) (0.28.5)
Requirement already satisfied: numpy in c:\users\jacob\anaconda3\lib\site-packages (from ripser) (1.15.2)
Requirement already satisfied: scipy in c:\users\jacob\anaconda3\lib\site-packages (from ripser) (1.1.0)
Requirement already satisfied: matplotlib in c:\users\jacob\anaconda3\lib\site-packages (from ripser) (2.2.3)
Requirement already satisfied: scikit-learn in c:\users\jacob\anaconda3\lib\site-packages (from ripser) (0.19.2)
Requirement already satisfied: cycler>=0.10 in c:\users\jacob\anaconda3\lib\site-packages (from matplotlib->ripser) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in c:\users\jacob\anaconda3\lib\site-packages (from matplotlib->ripser) (2.2.0)
Requirement already satisfied: python-dateutil>=2.1 in c:\users\jacob\anaconda3\lib\site-packages (from matplotlib->ripser) (2.7.3)
Requirement already satisfied: pytz in c:\users\jacob\anaconda3\lib\site-packages (from matplotlib->ripser) (2018.5)
Requirement already satisfied: six>=1.10 in c:\users\jacob\anaconda3\lib\site-packages (from matplotlib->ripser) (1.11.0)
Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\jacob\anaconda3\lib\site-packages (from matplotlib->ripser) (1.0.1)
Requirement already satisfied: setuptools in c:\users\jacob\anaconda3\lib\site-packages (from kiwisolver>=1.0.1->matplotlib->ripser) (40.4.3)
Skipping bdist_wheel for ripser, due to binaries being disabled for it.
Installing collected packages: ripser
  Running setup.py install for ripser ... error
    Complete output from command c:\users\jacob\anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\jacob\\AppData\\Local\\Temp\\pip-install-y5svum36\\ripser\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" build_ext --compiler=mingw32 install --record C:\Users\jacob\AppData\Local\Temp\pip-record-_iag3n9o\install-record.txt --single-version-externally-managed --compile:
    running build_ext
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\jacob\AppData\Local\Temp\pip-install-y5svum36\ripser\setup.py", line 77, in <module>
        cmdclass={'build_ext': CustomBuildExtCommand},
      File "c:\users\jacob\anaconda3\lib\site-packages\setuptools\__init__.py", line 140, in setup
        return distutils.core.setup(**attrs)
      File "c:\users\jacob\anaconda3\lib\distutils\core.py", line 148, in setup
        dist.run_commands()
      File "c:\users\jacob\anaconda3\lib\distutils\dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "c:\users\jacob\anaconda3\lib\distutils\dist.py", line 985, in run_command
        cmd_obj.run()
      File "C:\Users\jacob\AppData\Local\Temp\pip-install-y5svum36\ripser\setup.py", line 49, in run
        build_ext.run(self)
      File "c:\users\jacob\anaconda3\lib\site-packages\Cython\Distutils\old_build_ext.py", line 186, in run
        _build_ext.build_ext.run(self)
      File "c:\users\jacob\anaconda3\lib\distutils\command\build_ext.py", line 308, in run
        force=self.force)
      File "c:\users\jacob\anaconda3\lib\distutils\ccompiler.py", line 1031, in new_compiler
        return klass(None, dry_run, force)
      File "c:\users\jacob\anaconda3\lib\distutils\cygwinccompiler.py", line 285, in __init__
        CygwinCCompiler.__init__ (self, verbose, dry_run, force)
      File "c:\users\jacob\anaconda3\lib\distutils\cygwinccompiler.py", line 129, in __init__
        if self.ld_version >= "2.10.90":
    TypeError: '>=' not supported between instances of 'NoneType' and 'str'

    ----------------------------------------
Command "c:\users\jacob\anaconda3\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\jacob\\AppData\\Local\\Temp\\pip-install-y5svum36\\ripser\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" build_ext --compiler=mingw32 install --record C:\Users\jacob\AppData\Local\Temp\pip-record-_iag3n9o\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\jacob\AppData\Local\Temp\pip-install-y5svum36\ripser\

[sauln]

This SO thread might have the solution: https://stackoverflow.com/a/45096737/8054875

[ctralie]

Hi all, I'm a bit confused. Why are you trying to compile from source? We have prebuilt binaries on pypi. The mingw runtimes don't work with that?

…

On Thu, Oct 11, 2018, 8:07 PM Nathaniel Saul ***@***.***> wrote: This SO thread might have the solution: https://stackoverflow.com/a/45096737/8054875 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#49 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABNh5j1QjQ_wdUHe2WRaGKbuHl7GJpluks5uj4jkgaJpZM4XVltZ> .

[JacobPfau]

In the end I used linux instead, and installation worked fine.

[ctralie]

Okay sorry for the trouble!

…

On Mon, Oct 15, 2018, 12:39 PM Jacob ***@***.***> wrote: In the end I used linux instead, and installation worked fine. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#49 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABNh5mCNEFINCBWUr20hGY4Cj8WuL14eks5ulLpcgaJpZM4XVltZ> .

[jiadongdan]

Is there any python 3.7 version of wheel file? I am on windows too, cp36 said not a support on this platform.

[jiadongdan]

Is it possible to make pip install work on windows by modifying the setup file?

[sauln]

@GeekMe93 I'm working on Python 3.7 wheels and will try to have them up before the end of the ay.

[kezard]

Hi, I can pip ripser 0.6.0 successfully, but when I import it in the compile error comes:

I can't get the package "pyRipser" or It has been removed? so I can't call the package"ripser" successfuly... Is there anybody has the same problem with me ?

[ctralie]

@sauln It seems like it's not building the cython modules here. I thought the MANIFEST.in file would take care of this https://github.com/scikit-tda/ripser.py/blob/master/MANIFEST.in but this always seems to come up again...

…

On Sun, Nov 22, 2020 at 8:25 AM kezard ***@***.***> wrote: Hi, I can pip ripser 0.6.0 successfully, but when I import it in the compile error comes: [image: image] <https://user-images.githubusercontent.com/57929197/99904987-04000d80-2d09-11eb-8040-d2d1d75695be.png> I can't get the package "pyRipser" or It has been removed? so I can't call the package"ripser" successfuly... Is there anybody has the same problem with me ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#49 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJWDZUIRSADIPYKNHU5F63SREGMLANCNFSM4F2WLNMQ> .