https://github.com/pydata/pandas/issues/10608 I get the "pyobject_cmp not built" error when trying to import pandas in a virtualenv using the system python 3.5, dev-lang/python-3.5.1-r2, (or system python 2.7: dev-lang/python-2.7.11-r2), but no system libraries. I don't get this error if I use portage to build pandas, but reproducible science is a lot simpler using virtualenvs. Strangely, if I build a local version of python-3.5.1 (just downloading the tarball and typing configure; make altinstall prefix=/home/grant/mypython3 exec-prefix=/home/grant/python3), then a virtualenv pointing to the local python can install and import pandas just fine. Here's the log of the failing pandas import with the system python: feynman ~ > mkvirtualenv --python=/usr/bin/python3.5 clean35 Running virtualenv with interpreter /usr/bin/python3.5 Using base prefix '/usr' New python executable in clean35/bin/python3.5 Also creating executable in clean35/bin/python Installing setuptools, pip, wheel...done. (clean35)feynman ~ > rm ~/.cache/pip -rf (clean35)feynman ~ > pip install -U pip setuptools wheel Collecting pip Downloading pip-8.0.2-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 381kB/s Collecting setuptools Downloading setuptools-19.6.2-py2.py3-none-any.whl (472kB) 100% |████████████████████████████████| 475kB 962kB/s Collecting wheel Downloading wheel-0.26.0-py2.py3-none-any.whl (63kB) 100% |████████████████████████████████| 65kB 5.3MB/s Installing collected packages: pip, setuptools, wheel Found existing installation: pip 7.1.2 Uninstalling pip-7.1.2: Successfully uninstalled pip-7.1.2 Found existing installation: setuptools 18.2 Uninstalling setuptools-18.2: Successfully uninstalled setuptools-18.2 Found existing installation: wheel 0.24.0 Uninstalling wheel-0.24.0: Successfully uninstalled wheel-0.24.0 Successfully installed pip-8.0.2 setuptools-19.6.2 wheel-0.26.0 (clean35)feynman ~ > pip install pandas Collecting pandas Downloading pandas-0.17.1.tar.gz (6.7MB) 100% |████████████████████████████████| 6.7MB 72kB/s Collecting python-dateutil>=2 (from pandas) Downloading python_dateutil-2.4.2-py2.py3-none-any.whl (188kB) 100% |████████████████████████████████| 192kB 1.7MB/s Collecting pytz>=2011k (from pandas) Downloading pytz-2015.7-py2.py3-none-any.whl (476kB) 100% |████████████████████████████████| 479kB 884kB/s Collecting numpy>=1.7.0 (from pandas) Downloading numpy-1.10.4.tar.gz (4.1MB) 100% |████████████████████████████████| 4.1MB 102kB/s Collecting six>=1.5 (from python-dateutil>=2->pandas) Downloading six-1.10.0-py2.py3-none-any.whl Building wheels for collected packages: pandas, numpy Running setup.py bdist_wheel for pandas ... done Stored in directory: /home/grant/.cache/pip/wheels/21/92/81/0259bc54d3f52003b6b94825569abf890237f20c2122a2af4f Running setup.py bdist_wheel for numpy ... done Stored in directory: /home/grant/.cache/pip/wheels/66/f5/d7/f6ddd78b61037fcb51a3e32c9cd276e292343cdd62d5384efd Successfully built pandas numpy Installing collected packages: six, python-dateutil, pytz, numpy, pandas Successfully installed numpy-1.10.4 pandas-0.17.1 python-dateutil-2.4.2 pytz-2015.7 six-1.10.0 (clean35)feynman ~ > python Python 3.5.1 (default, Feb 2 2016, 12:02:14) [GCC 5.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import sys >>> sys.path ['', '/home/grant/Envs/clean35/lib64/python35.zip', '/home/grant/Envs/clean35/lib64/python3.5', '/home/grant/Envs/clean35/lib64/python3.5/plat-linux', '/home/grant/Envs/clean35/lib64/python3.5/lib-dynload', '/usr/lib64/python3.5', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-linux', '/home/grant/Envs/clean35/lib/python3.5/site-packages'] >>> import pandas as pd Traceback (most recent call last): File "/home/grant/Envs/clean35/lib/python3.5/site-packages/pandas/__init__.py", line 7, in <module> from pandas import hashtable, tslib, lib ImportError: /home/grant/Envs/clean35/lib/python3.5/site-packages/pandas/hashtable.cpython-35m-x86_64-linux-gnu.so: undefined symbol: pyobject_cmp During handling of the above exception, another exception occurred: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/grant/Envs/clean35/lib/python3.5/site-packages/pandas/__init__.py", line 13, in <module> "extensions first.".format(module)) ImportError: C extension: /home/grant/Envs/clean35/lib/python3.5/site-packages/pandas/hashtable.cpython-35m-x86_64-linux-gnu.so: undefined symbol: pyobject_cmp not built. If you want to import pandas from the source directory, you may need to run 'python setup.py build_ext --inplace' to build the C extensions first. If anybody has any ideas, I'd be grateful! Thanks, Grant
Nothing we can do. Upstream is aware and suggests to use conda.
Fixed by upstream some time ago.
