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brentp / fishers_exact_test

Fishers Exact Test for Python (Cython)
BSD 3-Clause "New" or "Revised" License
62 stars 21 forks source link

Build issue on Windows #16

Open deto opened 8 years ago

deto commented 8 years ago

I'm getting an error trying to install this on Windows. At first I tried this using conda, and after it failed there, I tried using just a barebones python2.7 install.

It seems that the issue stems from the fact that the Visual C++ for Python compiler that Microsoft released does not include an lgamma in its math.h

This appears to be the only issue. If I just replace the call to lgamma (in cfisher.c) with '0', then the package builds just fine.

See output from building a wheel below.

C:\Users\David\fishers_exact_test>C:\Python27\Scripts\pip.exe wheel --wheel-dir=wheel .
Processing c:\users\david\fishers_exact_test
Building wheels for collected packages: fisher
  Running setup.py bdist_wheel for fisher ... error
  Complete output from command c:\python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\david\\appdata\\local\\temp\\pip-cljy6z-build\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d c:\users\david\appdata\local\temp\tmpih00pjpip-wheel-:
  running bdist_wheel
  running build
  running build_py
  running build_ext
  building 'fisher.cfisher' extension
  creating build\temp.win-amd64-2.7
  creating build\temp.win-amd64-2.7\Release
  creating build\temp.win-amd64-2.7\Release\src
  C:\Users\David\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -Ic:\python27\lib\site-packages\numpy\core\include -Ic:\python27\include -Ic:\python27\PC /Tcsrc/cfisher.c /Fobuild\temp.win-amd64-2.7\Release\src/cfisher.obj -O3
  cl : Command line warning D9002 : ignoring unknown option '-O3'
  cfisher.c
  c:\python27\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
  src/cfisher.c(2106) : warning C4013: 'lgamma' undefined; assuming extern returning int
  src/cfisher.c(3442) : warning C4244: '=' : conversion from 'npy_intp' to 'int', possible loss of data
  C:\Users\David\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\amd64\link.exe /DLL /nologo /INCREMENTAL:NO /LIBPATH:c:\python27\libs /LIBPATH:c:\python27\PCbuild\amd64 /LIBPATH:c:\python27\PC\VS9.0\amd64 /EXPORT:initcfisher build\temp.win-amd64-2.7\Release\src/cfisher.obj /OUT:build\lib.win-amd64-2.7\fisher\cfisher.pyd /IMPLIB:build\temp.win-amd64-2.7\Release\src\cfisher.lib /MANIFESTFILE:build\temp.win-amd64-2.7\Release\src\cfisher.pyd.manifest
  cfisher.obj : warning LNK4197: export 'initcfisher' specified multiple times; using first specification
     Creating library build\temp.win-amd64-2.7\Release\src\cfisher.lib and object build\temp.win-amd64-2.7\Release\src\cfisher.exp
  cfisher.obj : error LNK2019: unresolved external symbol lgamma referenced in function __pyx_f_7cfisher_lnfactorial
  build\lib.win-amd64-2.7\fisher\cfisher.pyd : fatal error LNK1120: 1 unresolved externals
  error: command 'C:\\Users\\David\\AppData\\Local\\Programs\\Common\\Microsoft\\Visual C++ for Python\\9.0\\VC\\Bin\\amd64\\link.exe' failed with exit status 1120

  ----------------------------------------
  Failed building wheel for fisher
  Running setup.py clean for fisher
Failed to build fisher
ERROR: Failed to build one or more wheels
brentp commented 8 years ago

maybe we need:

extra_compile_args = ['-O3', '-std=c99']

in setup.py (line 10)

can you try that and let me know if it works. I don't have access to a windows machine for testing.

deto commented 8 years ago

Didn't help. The real issue seems to be that there just isn't any lgamma function in math.h for the Windows C compiler. To verify, I opened the file myself on my system and yep, definitely no lgamma.

See here for a compatibility table: http://www.johndcook.com/blog/math_h/

It seems to be the only function that's causing an issue, though. It all builds if I just remove lgamma (though of course, it's non-functional then).

It looks like there used to be an "lngamma" function, defined in the fischer source, that took care of this. I imagine the best solution would be to sense if lgamma exists and if not, use a fallback, though I don't know if there is an easy way to set that up in Cython.

On Wed, May 11, 2016 at 12:54 PM, Brent Pedersen - Bioinformatics < notifications@github.com> wrote:

maybe we need:

extra_compile_args = ['-O3', '-std=c99']

in setup.py (line 10)

can you try that and let me know if it works. I don't have access to a windows machine for testing.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/brentp/fishers_exact_test/issues/16#issuecomment-218570752

brentp commented 8 years ago

this is from 398c8ca by @superbobry . can you have a look?

superbobry commented 8 years ago

I thought npy_math.h has lgamma but it doesn't, so the best way would be to simply resurrect the hand-rolled version.

deto commented 8 years ago

Yes, looks like scipy has it - http://docs.scipy.org/doc/scipy/reference/generated/scipy.special.gammaln.html#scipy.special.gammaln - though not sure how hard it would be to borrow the implementation. Or if it really is worth the effort - performance-wise.

gursimar commented 7 years ago

Guys, any luck getting this work on windows?