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choderalab / pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)
http://pymbar.readthedocs.io
MIT License
235 stars 91 forks source link

Pip install seems not to work for OS X #174

Open mrshirts opened 9 years ago

mrshirts commented 9 years ago

I get the following error messages. Seems to just be an issue with compiling the helper code, so will go away with 3.0.

Collecting pymbar Using cached pymbar-2.1.0-beta.tar.gz author Michael R. Shirts and John D. Chodera author_email michael.shirts@virginia.edu, choderaj@mskcc.org data_files [] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [<setuptools.extension.Extension instance at 0x101951128>] license GPL 2.0 long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar'} packages ['pymbar', 'pymbar.testsystems'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'nose'] url http://github.com/choderalab/pymbar version 2.1.0-beta Installing collected packages: pymbar Running setup.py install for pymbar author Michael R. Shirts and John D. Chodera author_email michael.shirts@virginia.edu, choderaj@mskcc.org data_files [] descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method. download_url http://github.com/choderalab/pymbar ext_modules [<setuptools.extension.Extension instance at 0x102347ea8>] license GPL 2.0 long_description Pymbar (https://simtk.org/home/pymbar) is a library that provides tools for optimally combining simulations from multiple thermodynamic states using maximum likelihood methods to compute free energies (normalization constants) and expectation values from all of the samples simultaneously. name pymbar package_dir {'pymbar': 'pymbar'} packages ['pymbar', 'pymbar.testsystems'] platforms ['Linux', 'Mac OS X', 'Windows'] requires ['numpy', 'scipy', 'nose'] url http://github.com/choderalab/pymbar version 2.1.0-beta building '_pymbar' extension gcc -fno-strict-aliasing -I/Users/mrshirts/anaconda/include -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/mrshirts/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/mrshirts/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ -I/Users/mrshirts/anaconda/include/python2.7 -c pymbar/_pymbar.c -o build/temp.macosx-10.5-x86_64-2.7/pymbar/_pymbar.o -std=c99 -O2 -shared -msse2 -msse3 In file included from /opt/local/lib/gcc47/gcc/x86_64-apple-darwin14/4.7.4/include/stdint.h:3:0, from /Developer/SDKs/MacOSX10.5.sdk/usr/include/inttypes.h:255, from /Users/mrshirts/anaconda/include/python2.7/pyport.h:9, from /Users/mrshirts/anaconda/include/python2.7/Python.h:58, from pymbar/_pymbar.c:80: /opt/local/lib/gcc47/gcc/x86_64-apple-darwin14/4.7.4/include-fixed/stdint.h:27:32: fatal error: sys/_types/_int8_t.h: No such file or directory compilation terminated. error: command 'gcc' failed with exit status 1 Complete output from command /Users/mrshirts/anaconda/bin/python -c "import setuptools, tokenize;file='/private/var/folders/4v/g0zjp6c95535931grpmdq5840000gp/T/pip-build-lEEu3I/pymbar/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /var/folders/4v/g0zjp6c95535931grpmdq5840000gp/T/pip-9hZI4Z-record/install-record.txt --single-version-externally-managed --compile: author Michael R. Shirts and John D. Chodera

                            author_email             michael.shirts@virginia.edu, choderaj@mskcc.org

                              data_files                                                          []

                             descriptionPython implementation of the multistate Bennett acceptance ratio (MBAR) method.

                            download_url                         http://github.com/choderalab/pymbar

                             ext_modules  [<setuptools.extension.Extension instance at 0x102347ea8>]

                                 license                                                     GPL 2.0

                        long_description

    Pymbar (https://simtk.org/home/pymbar) is a library

    that provides tools for optimally combining simulations

    from multiple thermodynamic states using maximum likelihood

    methods to compute free energies (normalization constants)

    and expectation values from all of the samples simultaneously.

                                    name                                                      pymbar

                             package_dir                                        {'pymbar': 'pymbar'}

                                packages                            ['pymbar', 'pymbar.testsystems']

                               platforms                            ['Linux', 'Mac OS X', 'Windows']

                                requires                                  ['numpy', 'scipy', 'nose']

                                     url                         http://github.com/choderalab/pymbar

                                 version                                                  2.1.0-beta

running install

running build

running build_py

creating build

creating build/lib.macosx-10.5-x86_64-2.7

creating build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/bar.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/confidenceintervals.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/exp.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/mbar.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/timeseries.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/utils.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/utils_for_testing.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

copying pymbar/version.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar

creating build/lib.macosx-10.5-x86_64-2.7/pymbar/testsystems

copying pymbar/testsystems/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar/testsystems

copying pymbar/testsystems/exponential_distributions.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar/testsystems

copying pymbar/testsystems/gaussian_work.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar/testsystems

copying pymbar/testsystems/harmonic_oscillators.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar/testsystems

copying pymbar/testsystems/timeseries.py -> build/lib.macosx-10.5-x86_64-2.7/pymbar/testsystems

running build_ext

building '_pymbar' extension

creating build/temp.macosx-10.5-x86_64-2.7

creating build/temp.macosx-10.5-x86_64-2.7/pymbar

gcc -fno-strict-aliasing -I/Users/mrshirts/anaconda/include -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/mrshirts/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/mrshirts/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ -I/Users/mrshirts/anaconda/include/python2.7 -c pymbar/_pymbar.c -o build/temp.macosx-10.5-x86_64-2.7/pymbar/_pymbar.o -std=c99 -O2 -shared -msse2 -msse3

In file included from /opt/local/lib/gcc47/gcc/x86_64-apple-darwin14/4.7.4/include/stdint.h:3:0,

                 from /Developer/SDKs/MacOSX10.5.sdk/usr/include/inttypes.h:255,

                 from /Users/mrshirts/anaconda/include/python2.7/pyport.h:9,

                 from /Users/mrshirts/anaconda/include/python2.7/Python.h:58,

                 from pymbar/_pymbar.c:80:

/opt/local/lib/gcc47/gcc/x86_64-apple-darwin14/4.7.4/include-fixed/stdint.h:27:32: fatal error: sys/_types/_int8_t.h: No such file or directory

compilation terminated.

error: command 'gcc' failed with exit status 1

----------------------------------------
Command "/Users/mrshirts/anaconda/bin/python -c "import setuptools, tokenize;__file__='/private/var/folders/4v/g0zjp6c95535931grpmdq5840000gp/T/pip-build-lEEu3I/pymbar/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/4v/g0zjp6c95535931grpmdq5840000gp/T/pip-9hZI4Z-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/4v/g0zjp6c95535931grpmdq5840000gp/T/pip-build-lEEu3I/pymbar
jchodera commented 9 years ago

This looks like some sort of local compiler installation issue where your stdint.h is including files that are somehow not installed.

What if we remove pymbar from pip and go exclusively to conda? This will prevent these kinds of issues completely.

kyleabeauchamp commented 9 years ago

I'm OK with that plan--novices should be using conda anyway, and advanced users don't really have a barrier to grabbing the release source tarball.