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I tried all answers but I can't solve the problem of installing Biopython package I installed Mingw , but when I try to install the package : python setup.py install I get the following error:

    running install
    running build
    running build_py
    running build_ext
    building 'Bio.cpairwise2' extension
    c:\mingw\bin\gcc.exe -mno-cygwin -mdll -O -Wall -Ic:\Python33\include -Ic:\Pytho
    n33\include -c Bio/cpairwise2module.c -o build\temp.win-amd64-3.3\Release\bio\cp
    airwise2module.o
    writing build\temp.win-amd64-3.3\Release\bio\cpairwise2.def
    c:\mingw\bin\gcc.exe -mno-cygwin -shared -s build\temp.win-amd64-3.3\Release\bio
    \cpairwise2module.o build\temp.win-amd64-3.3\Release\bio\cpairwise2.def -Lc:\Pyt
    hon33\libs -Lc:\Python33\PCbuild\amd64 -lpython33 -lmsvcr100 -o build\lib.win-am
    d64-3.3\Bio\cpairwise2.pyd
    c:/mingw/bin/../lib/gcc/mingw32/4.3.3/../../../../mingw32/bin/ld.exe: c:\Python3
    3\libs/python33.lib(python33.dll): Recognised but unhandled machine type (0x8664
    ) in Import Library Format archive
    c:/mingw/bin/../lib/gcc/mingw32/4.3.3/../../../../mingw32/bin/ld.exe: cannot fin
    d -lmsvcr100
    collect2: ld returned 1 exit status

error: command 'gcc' failed with exit status 1
user3216969
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  • You are probably missing the Microsoft C++ libraries: http://www.microsoft.com/en-us/download/details.aspx?id=13523 On the other hand, I wonder if you can compile a python extension with MinGW. The official documentation suggests MS Visual Studio 2010 for Python 3.3. – Cilyan Feb 05 '14 at 01:04

2 Answers2

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According to here for error: cannot find -lmsvcr100 you need to first install Microsoft Visual C++ 2010 Redistributable Package, and second, copy the msvcr100.dll to C:\Python33\libs the directory for linking is C:\Python44\libs because both -lpython and -lmsvcr100 are pointed to the same location during compilation, and so they have to be in the same directory.` This solution worked for me when I needed to install Cython.

the_prole
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-1

You will get two errors. The first is yours:

error: cannot find -lmsvcr100
error: command 'gcc' failed with exit status 1

Then you will get a second error after you solve the first one:

error: unrecognized command line option '-mno-cygwin'
error: command 'gcc' failed with exit status 1

They are two different errors with two different solutions. You can find more here.

user4261180
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