pybedtools-0.6.1build error

[aihardin]

Hi! I'm trying to install on OSX 10.8.2 with gcc 4.2 and Python 2.7.3 -- EPD 7.3-1 (32-bit).

when I try to install with pip or easy_install I get a error:

easy_install pybedtools
Searching for pybedtools
Reading http://pypi.python.org/simple/pybedtools/
Reading http://pypi.python.org/simple/pybedtools/none
Best match: pybedtools 0.6.1
Downloading http://pypi.python.org/packages/source/p/pybedtools/pybedtools-0.6.1.tar.gz#md5=c67a34e48deb8d747795be09f9bc3dd6
Processing pybedtools-0.6.1.tar.gz
Writing /var/folders/1j/lkx2dg7d7tn6f4t4c6lwmt9r0000gq/T/easy_install-TLOphz/pybedtools-0.6.1/setup.cfg
Running pybedtools-0.6.1/setup.py -q bdist_egg --dist-dir /var/folders/1j/lkx2dg7d7tn6f4t4c6lwmt9r0000gq/T/easy_install-TLOphz/pybedtools-0.6.1/egg-dist-tmp-j83m23
warning: pybedtools/cbedtools.pyx:596:16: Unreachable code
src/bedFile.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits, _Alloc = std::allocator]’:
src/bedFile.cpp:41: instantiated from here
src/bedFile.cpp:41: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits, _Alloc = std::allocator]’ but no definition available
src/bedFile.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits, _Alloc = std::allocator]’:
src/bedFile.cpp:41: instantiated from here
src/bedFile.cpp:41: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits, _Alloc = std::allocator]’ but no definition available
src/bedFile.cpp: In instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits, _Alloc = std::allocator]’:
src/bedFile.cpp:41: instantiated from here
src/bedFile.cpp:41: error: explicit instantiation of ‘std::basic_ostream<_CharT, _Traits>& std::operator<<(std::basic_ostream<_CharT, _Traits>&, const std::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char, _Traits = std::char_traits, _Alloc = std::allocator]’ but no definition available
error: Setup script exited with error: command 'gcc' failed with exit status 1

[daler]

Thanks for reporting this. It's the first time I've heard of this issue . . .can you try the fix described here? :

http://stackoverflow.com/questions/11748504/trying-to-build-muparser-error-explicit-instantiation-of-stdbasic-ostream-b

[aihardin]

Thanks for the suggestion! It didn't work directly but got me on the right path. I tried CFLAGS=-mmacosx-version-min=10.7 pip install pybedtools which complain quite a bit initially. I think the issue was that I had removed my old Xcode installation from /Developer since the latest Xcode runs in an App folder. Following http://lunokhod.org/?p=269, I was able to recover some old SDKs and get it to work.