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pandas-dev / pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
https://pandas.pydata.org
BSD 3-Clause "New" or "Revised" License
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Segmentation fault #16473

Closed oxhaowang closed 7 years ago

oxhaowang commented 7 years ago

Problem Description

For latest 0.20.1 version I got: 

>>> import pandas
Segmentation fault (core dumped)

When I rolled back to version 0.19.2, the import line works fine but not the test function, see:

$ python3
Python 3.5.2 (default, Nov 17 2016, 17:05:23) 
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas
>>> import pandas as pd
>>> pd.test()
Running unit tests for pandas
pandas version 0.19.2
numpy version 1.12.1
pandas is installed in /usr/local/lib/python3.5/dist-packages/pandas
Python version 3.5.2 (default, Nov 17 2016, 17:05:23) [GCC 5.4.0 20160609]
nose version 1.3.7
Segmentation fault (core dumped)

This might not be a pandas issue after all. I am posting this in case anyone got any clues..

Other installed python3 modules on my machine are

alabaster==0.7.10 apiclient==1.0.3 appdirs==1.4.3 apsw==3.9.2.post1 apturl==0.5.2 asn1crypto==0.22.0 astroid==1.5.2 astropy==1.3.2 Babel==2.4.0 beautifulsoup4==4.6.0 bleach==2.0.0 blinker==1.4 blosc==1.5.1 bokeh==0.12.5 boto==2.46.1 bottle==0.12.13 Bottleneck==1.2.1 branca==0.2.0 Brlapi==0.6.4 cffi==1.10.0 chardet==3.0.3 checkbox-support==0.33.0 colorama==0.3.9 command-not-found==0.3 corner==2.0.1 CProfileV==1.0.7 cryptography==1.8.1 cycler==0.10.0 Cython==0.25.2 decorator==4.0.11 defer==1.0.6 demjson==2.2.4 docutils==0.13.1 emcee==2.2.1 entrypoints==0.2.2 et-xmlfile==1.0.1 fbprophet==0.1.1 feedparser==5.2.1 flake8==3.3.0 folium==0.3.0 googlefinance==0.7 guacamole==0.9.2 h5py==2.7.0 html5lib==0.999999999 httplib2==0.10.3 idna==2.5 imagesize==0.7.1 inflection==0.3.1 ipykernel==4.6.1 ipython==6.0.0 ipython-genutils==0.2.0 ipywidgets==6.0.0 isort==4.2.5 jdcal==1.3 jedi==0.10.2 Jinja2==2.9.6 jsonschema==2.6.0 jupyter==1.0.0 jupyter-client==5.0.1 jupyter-console==5.1.0 jupyter-core==4.3.0 Keras==2.0.4 language-selector==0.1 lazy-object-proxy==1.3.1 line-profiler==2.0 louis==2.6.4 lxml==3.7.3 mahotas==1.4.3 Mako==1.0.6 Markdown==2.6.8 Markdown-Editor==1.0.3 MarkupSafe==1.0 matplotlib==2.0.2 mccabe==0.6.1 memory-profiler==0.47 mistune==0.7.4 more-itertools==3.0.0 nbconvert==5.1.1 nbformat==4.3.0 ndg-httpsclient==0.4.2 networkx==1.11 nltk==3.2.4 nose==1.3.7 notebook==5.0.0 numexpr==2.6.2 numpy==1.12.1 numpydoc==0.6.0 oauthlib==2.0.2 olefile==0.44 onboard==1.2.0 openpyxl==2.4.7 packaging==16.8 padme==1.1.1 pandas==0.19.2 pandas-datareader==0.4.0 pandocfilters==1.4.1 patsy==0.4.1 pep8==1.7.0 pexpect==4.2.1 pickleshare==0.7.4 Pillow==4.1.1 plainbox==0.34.0 prompt-toolkit==1.0.14 protobuf==3.3.0 psutil==5.2.2 psycopg2==2.7.1 ptyprocess==0.5.1 pyasn1==0.2.3 pycallgraph==1.0.1 pycodestyle==2.3.1 pycparser==2.17 pycups==1.9.73 pycurl==7.43.0 pyenchant==1.6.8 pyflakes==1.5.0 Pygments==2.2.0 pygobject==3.20.0 pygtkspellcheck==4.0.5 PyJWT==1.5.0 pylint==1.7.1 pymdown-extensions==3.2 PyMySQL==0.7.11 PyOpenGL==3.1.0 pyOpenSSL==17.0.0 pyparsing==2.2.0 PyQt5==5.8.2 pyqtgraph==0.10.0 pysmbc==1.0.15.5 pystan==2.15.0.1 python-apt==1.1.0b1 python-dateutil==2.6.0 python-debian==0.1.28 python-systemd==231 python-termstyle==0.1.10 pytz==2017.2 pyxdg==0.25 PyYAML==3.12 pyzmq==16.0.2 QtAwesome==0.4.4 qtconsole==4.3.0 QtPy==1.2.1 Quandl==3.1.0 rednose==1.2.2 requests==2.14.2 requests-file==1.4.2 requests-ftp==0.3.1 roman==2.0.0 rope-py3k==0.9.4.post1 scikit-fuzzy==0.2 scikit-learn==0.18.1 scipy==0.19.0 screen-resolution-extra==0.0.0 seaborn==0.7.1 sessioninstaller==0.0.0 simplegeneric==0.8.1 sip==4.19.2 six==1.10.0 sklearn==0.0 snowballstemmer==1.2.1 Sphinx==1.6.1 sphinx-rtd-theme==0.2.4 sphinxcontrib-websupport==1.0.1 spyder==3.1.4 SQLAlchemy==1.1.10 statsmodels==0.8.0 system-service==0.3 tables==3.4.2 tensorflow==1.1.0 terminado==0.6 termstyle==0.1.11 testpath==0.3 Theano==0.9.0 tornado==4.5.1 traitlets==4.3.2 tushare==0.5.0 typing==3.6.1 ubuntu-drivers-common==0.0.0 ufw==0.35 unattended-upgrades==0.1 unity-scope-calculator==0.1 unity-scope-chromiumbookmarks==0.1 unity-scope-colourlovers==0.1 unity-scope-devhelp==0.1 unity-scope-firefoxbookmarks==0.1 unity-scope-gdrive==0.7 unity-scope-manpages==0.1 unity-scope-openclipart==0.1 unity-scope-texdoc==0.1 unity-scope-tomboy==0.1 unity-scope-virtualbox==0.1 unity-scope-yelp==0.1 unity-scope-zotero==0.1 urllib3==1.21.1 usb-creator==0.3.0 wcwidth==0.1.7 webencodings==0.5.1 Werkzeug==0.12.2 widgetsnbextension==2.0.0 wrapt==1.10.10 wxPython-Phoenix==3.0.3 xarray==0.9.5 xdiagnose==3.8.4.1 xkit==0.0.0 xlrd==1.0.0 XlsxWriter==0.9.6 xlwt==1.2.0

Output of pd.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.5.2.final.0 python-bits: 64 OS: Linux OS-release: 4.4.0-78-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: en_GB.UTF-8 pandas: 0.19.2 nose: 1.3.7 pip: 9.0.1 setuptools: 35.0.2 Cython: 0.25.2 numpy: 1.12.1 scipy: 0.19.0 statsmodels: 0.8.0 xarray: 0.9.5 IPython: 6.0.0 sphinx: 1.6.1 patsy: 0.4.1 dateutil: 2.6.0 pytz: 2017.2 blosc: 1.5.1 bottleneck: 1.2.1 tables: 3.4.2 numexpr: 2.6.2 matplotlib: 2.0.2 openpyxl: 2.4.7 xlrd: 1.0.0 xlwt: 1.2.0 xlsxwriter: 0.9.6 lxml: 3.7.3 bs4: 4.6.0 html5lib: 0.999999999 httplib2: 0.10.3 apiclient: None sqlalchemy: 1.1.10 pymysql: 0.7.11.None psycopg2: 2.7.1 (dt dec pq3 ext lo64) jinja2: 2.9.6 boto: 2.46.1 pandas_datareader: 0.4.0
jreback commented 7 years ago

you have an installation problem. pls read the instructions here. conda install pandas or pip install pandas works.

oxhaowang commented 7 years ago

@jreback I did installed with pip...

blakeliu commented 6 years ago

wjy@wjy-Z270X-UD3:~/blake/medical/test$ conda install pandas Fetching package metadata ............... Solving package specifications: .

Package plan for installation in environment /home/wjy/anaconda3:

The following NEW packages will be INSTALLED:

pandas: 0.20.3-py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free

Proceed ([y]/n)? y

wjy@wjy-Z270X-UD3:~/blake/medical/test$ python Python 3.5.2 |Anaconda custom (64-bit)| (default, Jul 2 2016, 17:53:06) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux Type "help", "copyright", "credits" or "license" for more information.

import pandas import pandas as pd pd.test() running: pytest --skip-slow --skip-network /home/wjy/anaconda3/lib/python3.5/site-packages/pandas ============================ test session starts ============================= platform linux -- Python 3.5.2, pytest-2.9.2, py-1.4.31, pluggy-0.3.1 rootdir: /home/wjy/anaconda3/lib/python3.5/site-packages/pandas, inifile: collecting 6594 items / 2 skipped段错误 (核心已转储)