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From xxwang <xiaoni.w...@obspm.fr>
Subject Re: Pyarrow installation
Date Thu, 09 Jan 2020 14:42:37 GMT
Just to give complete information of errors:

ImportError                               Traceback (most recent call last)
<ipython-input-1-f1048abcb32d> in <module>
----> 1 import pyarrow

~/anaconda3/lib/python3.7/site-packages/pyarrow/__init__.py in <module>
     52 
     53 
---> 54 from pyarrow.lib import cpu_count, set_cpu_count
     55 from pyarrow.lib import (null, bool_,
     56                          int8, int16, int32, int64,

ImportError: ~/anaconda3/lib/python3.7/site-packages/pyarrow/lib.cpython-37m-x86_64-linux-gnu.so:
undefined symbol: _ZNK5arrow6Status8ToStringB5cxx11Ev



> Le 9 janv. 2020 à 15:40, xxwang <xiaoni.wang@obspm.fr> a écrit :
> 
> Hi Wes
>      Thanks. There seems to be a version conflict problem. I have the condo-forge in
my channel list. I had installed Pyarrow by 'conda install pyarrow’.
> What I did just now:
> 1) I removed Pyarrow by : conda uninstall pyarrow
> 2) Then I tried to reinstall Pyarrow by: conda install pyarrow
> The conda suggested to install Pyarrow-0.11.1. So I installed it. Then I got the same
error of 'undefined symbol'.
> 
> Thanks in advance,
> 
> Xiaoni
> 
> 
> conda list give:
> # packages in environment at /obs/xxwang/anaconda3:
> #
> # Name                    Version                   Build  Channel
> _ipyw_jlab_nb_ext_conf    0.1.0                    py37_0  
> _libgcc_mutex             0.1                        main  
> _tflow_select             2.3.0                       mkl  
> absl-py                   0.8.1                    py37_0  
> alabaster                 0.7.12                   py37_0  
> anaconda                  2019.10                  py37_0  
> anaconda-client           1.7.2                    py37_0  
> anaconda-navigator        1.9.7                    py37_0  
> anaconda-project          0.8.3                      py_0  
> aplus                     0.11.0                     py_1    conda-forge
> arrow-cpp                 0.11.1           py37h3bd774a_1    conda-forge
> asn1crypto                1.0.1                    py37_0  
> astor                     0.8.0                    py37_0  
> astroid                   2.3.1                    py37_0  
> astropy                   3.2.2            py37h7b6447c_0  
> atomicwrites              1.3.0                    py37_1  
> attrs                     19.2.0                     py_0  
> babel                     2.7.0                      py_0  
> backcall                  0.1.0                    py37_0  
> backports                 1.0                        py_2  
> backports.functools_lru_cache 1.6.1                      py_0  
> backports.os              0.1.1                    py37_0  
> backports.shutil_get_terminal_size 1.0.0                    py37_2  
> backports.tempfile        1.0                        py_1  
> backports.weakref         1.0.post1                  py_1  
> beautifulsoup4            4.8.0                    py37_0  
> binutils_impl_linux-64    2.33.1               he6710b0_7  
> binutils_linux-64         2.33.1              h9595d00_15  
> bitarray                  1.0.1            py37h7b6447c_0  
> bkcharts                  0.2                      py37_0  
> blas                      1.0                         mkl  
> bleach                    3.1.0                    py37_0  
> blosc                     1.16.3               hd408876_0  
> bokeh                     1.3.4                    py37_0  
> boost-cpp                 1.68.0            h11c811c_1000    conda-forge
> boto                      2.49.0                   py37_0  
> boto3                     1.10.39                    py_0  
> botocore                  1.13.39                    py_0  
> bottleneck                1.2.1            py37h035aef0_1  
> bqplot                    0.12.2                     py_0    conda-forge
> branca                    0.3.1                      py_0    conda-forge
> bzip2                     1.0.8                h7b6447c_0  
> c-ares                    1.15.0            h7b6447c_1001  
> ca-certificates           2019.8.28                     0  
> cachetools                3.1.1                      py_0    conda-forge
> cairo                     1.14.12              h8948797_3  
> certifi                   2019.9.11                py37_0  
> cffi                      1.12.3           py37h2e261b9_0  
> cftime                    1.0.4.2          py37hdd07704_0  
> chardet                   3.0.4                 py37_1003  
> click                     7.0                      py37_0  
> cloudpickle               1.2.2                      py_0  
> clyent                    1.2.2                    py37_1  
> colorama                  0.4.1                    py37_0  
> conda                     4.7.12                   py37_0  
> conda-build               3.18.9                   py37_3  
> conda-env                 2.6.0                         1  
> conda-package-handling    1.6.0            py37h7b6447c_0  
> conda-verify              3.4.2                      py_1  
> contextlib2               0.6.0                      py_0  
> cryptography              2.7              py37h1ba5d50_0  
> curl                      7.65.3               hbc83047_0  
> cycler                    0.10.0                   py37_0  
> cython                    0.29.13          py37he6710b0_0  
> cytoolz                   0.10.0           py37h7b6447c_0  
> dask                      2.5.2                      py_0  
> dask-core                 2.5.2                      py_0  
> dbus                      1.13.6               h746ee38_0  
> decorator                 4.4.0                    py37_1  
> defusedxml                0.6.0                      py_0  
> distributed               2.5.2                      py_0  
> docutils                  0.15.2                   py37_0  
> entrypoints               0.3                      py37_0  
> et_xmlfile                1.0.1                    py37_0  
> expat                     2.2.6                he6710b0_0  
> fastcache                 1.1.0            py37h7b6447c_0  
> filelock                  3.0.12                     py_0  
> flask                     1.1.1                      py_0  
> fontconfig                2.13.0               h9420a91_0  
> freetype                  2.9.1                h8a8886c_1  
> fribidi                   1.0.5                h7b6447c_0  
> fsspec                    0.5.2                      py_0  
> future                    0.18.2                   py37_0  
> gast                      0.2.2                    py37_0  
> gcc_impl_linux-64         7.3.0                habb00fd_1  
> gcc_linux-64              7.3.0               h553295d_15  
> get_terminal_size         1.0.0                haa9412d_0  
> gevent                    1.4.0            py37h7b6447c_0  
> git                       2.23.0          pl526hacde149_0  
> glib                      2.56.2               hd408876_0  
> glob2                     0.7                        py_0  
> gmp                       6.1.2                h6c8ec71_1  
> gmpy2                     2.0.8            py37h10f8cd9_2  
> google-pasta              0.1.8                      py_0  
> graphite2                 1.3.13               h23475e2_0  
> greenlet                  0.4.15           py37h7b6447c_0  
> grpcio                    1.16.1           py37hf8bcb03_1  
> gst-plugins-base          1.14.0               hbbd80ab_1  
> gstreamer                 1.14.0               hb453b48_1  
> gxx_impl_linux-64         7.3.0                hdf63c60_1  
> gxx_linux-64              7.3.0               h553295d_15  
> h5py                      2.9.0            py37h7918eee_0  
> harfbuzz                  1.8.8                hffaf4a1_0  
> hdf4                      4.2.13               h3ca952b_2  
> hdf5                      1.10.4               hb1b8bf9_0  
> heapdict                  1.0.1                      py_0  
> html5lib                  1.0.1                    py37_0  
> icu                       58.2                 h9c2bf20_1  
> idna                      2.8                      py37_0  
> imageio                   2.6.0                    py37_0  
> imagesize                 1.1.0                    py37_0  
> importlib_metadata        0.23                     py37_0  
> intel-openmp              2019.4                      243  
> ipydatawidgets            4.0.1                      py_0    conda-forge
> ipykernel                 5.1.2            py37h39e3cac_0  
> ipyleaflet                0.11.6                   py37_0    conda-forge
> ipympl                    0.3.3                      py_0  
> ipyscales                 0.3.0                      py_0    conda-forge
> ipython                   7.8.0            py37h39e3cac_0  
> ipython_genutils          0.2.0                    py37_0  
> ipyvolume                 0.5.2                    py37_0    conda-forge
> ipyvue                    1.0.2                      py_0    conda-forge
> ipyvuetify                1.1.1                      py_0    conda-forge
> ipywebrtc                 0.5.0                    py37_0    conda-forge
> ipywidgets                7.5.1                      py_0  
> isort                     4.3.21                   py37_0  
> itsdangerous              1.1.0                    py37_0  
> jbig                      2.1                  hdba287a_0  
> jdcal                     1.4.1                      py_0  
> jedi                      0.15.1                   py37_0  
> jeepney                   0.4.1                      py_0  
> jinja2                    2.10.3                     py_0  
> jmespath                  0.9.4                      py_0  
> joblib                    0.13.2                   py37_0  
> jpeg                      9b                   h024ee3a_2  
> json5                     0.8.5                      py_0  
> jsonschema                3.0.2                    py37_0  
> jupyter                   1.0.0                    py37_7  
> jupyter_client            5.3.3                    py37_1  
> jupyter_console           6.0.0                    py37_0  
> jupyter_core              4.5.0                      py_0  
> jupyterlab                1.1.4              pyhf63ae98_0  
> jupyterlab_server         1.0.6                      py_0  
> keras                     2.3.1                    py37_0    conda-forge
> keras-applications        1.0.8                      py_0  
> keras-preprocessing       1.1.0                      py_1  
> keyring                   18.0.0                   py37_0  
> kiwisolver                1.1.0            py37he6710b0_0  
> krb5                      1.16.1               h173b8e3_7  
> lazy-object-proxy         1.4.2            py37h7b6447c_0  
> ld_impl_linux-64          2.33.1               h53a641e_7  
> libarchive                3.3.3                h5d8350f_5  
> libcurl                   7.65.3               h20c2e04_0  
> libedit                   3.1.20181209         hc058e9b_0  
> libevent                  2.1.8                h1ba5d50_0  
> libffi                    3.2.1                hd88cf55_4  
> libgcc-ng                 9.1.0                hdf63c60_0  
> libgfortran-ng            7.3.0                hdf63c60_0  
> libgpuarray               0.7.6                h14c3975_0  
> liblief                   0.9.0                h7725739_2  
> libnetcdf                 4.6.1                h11d0813_2  
> libpng                    1.6.37               hbc83047_0  
> libprotobuf               3.11.2               hd408876_0  
> libsodium                 1.0.16               h1bed415_0  
> libssh2                   1.8.2                h1ba5d50_0  
> libstdcxx-ng              9.1.0                hdf63c60_0  
> libtiff                   4.0.10               h2733197_2  
> libtool                   2.4.6                h7b6447c_5  
> libuuid                   1.0.3                h1bed415_2  
> libxcb                    1.13                 h1bed415_1  
> libxml2                   2.9.9                hea5a465_1  
> libxslt                   1.1.33               h7d1a2b0_0  
> llvmlite                  0.29.0           py37hd408876_0  
> locket                    0.2.0                    py37_1  
> lxml                      4.4.1            py37hefd8a0e_0  
> lz4-c                     1.8.1.2              h14c3975_0  
> lzo                       2.10                 h49e0be7_2  
> mako                      1.1.0                      py_0  
> markdown                  3.1.1                    py37_0  
> markupsafe                1.1.1            py37h7b6447c_0  
> matplotlib                3.1.1            py37h5429711_0  
> mccabe                    0.6.1                    py37_1  
> mistune                   0.8.4            py37h7b6447c_0  
> mkl                       2019.4                      243  
> mkl-service               2.3.0            py37he904b0f_0  
> mkl_fft                   1.0.14           py37ha843d7b_0  
> mkl_random                1.1.0            py37hd6b4f25_0  
> mock                      3.0.5                    py37_0  
> more-itertools            7.2.0                    py37_0  
> mpc                       1.1.0                h10f8cd9_1  
> mpfr                      4.0.1                hdf1c602_3  
> mpmath                    1.1.0                    py37_0  
> msgpack-python            0.6.1            py37hfd86e86_1  
> multipledispatch          0.6.0                    py37_0  
> navigator-updater         0.2.1                    py37_0  
> nbconvert                 5.6.0                    py37_1  
> nbformat                  4.4.0                    py37_0  
> ncurses                   6.1                  he6710b0_1  
> netcdf4                   1.4.2            py37h808af73_0  
> networkx                  2.3                        py_0  
> nltk                      3.4.5                    py37_0  
> nose                      1.3.7                    py37_2  
> notebook                  6.0.1                    py37_0  
> numba                     0.45.1           py37h962f231_0  
> numexpr                   2.7.0            py37h9e4a6bb_0  
> numpy                     1.17.2           py37haad9e8e_0  
> numpy-base                1.17.2           py37hde5b4d6_0  
> numpydoc                  0.9.1                      py_0  
> olefile                   0.46                     py37_0  
> openpyxl                  3.0.0                      py_0  
> openssl                   1.1.1d               h7b6447c_2  
> opt_einsum                3.1.0                      py_0  
> packaging                 19.2                       py_0  
> pandas                    0.25.1           py37he6710b0_0  
> pandoc                    2.2.3.2                       0  
> pandocfilters             1.4.2                    py37_1  
> pango                     1.42.4               h049681c_0  
> parquet-cpp               1.5.1                         3    conda-forge
> parso                     0.5.1                      py_0  
> partd                     1.0.0                      py_0  
> patchelf                  0.9                  he6710b0_3  
> path.py                   12.0.1                     py_0  
> pathlib2                  2.3.5                    py37_0  
> patsy                     0.5.1                    py37_0  
> pcre                      8.43                 he6710b0_0  
> pep8                      1.7.1                    py37_0  
> perl                      5.26.2               h14c3975_0  
> pexpect                   4.7.0                    py37_0  
> pickleshare               0.7.5                    py37_0  
> pillow                    6.2.0            py37h34e0f95_0  
> pip                       19.2.3                   py37_0  
> pixman                    0.38.0               h7b6447c_0  
> pkginfo                   1.5.0.1                  py37_0  
> pluggy                    0.13.0                   py37_0  
> ply                       3.11                     py37_0  
> progressbar2              3.37.1                   py37_0  
> prometheus_client         0.7.1                      py_0  
> prompt_toolkit            2.0.10                     py_0  
> protobuf                  3.11.2           py37he6710b0_0  
> psutil                    5.6.3            py37h7b6447c_0  
> ptyprocess                0.6.0                    py37_0  
> py                        1.8.0                    py37_0  
> py-lief                   0.9.0            py37h7725739_2  
> pyarrow                   0.11.1          py37hbbcf98d_1002    conda-forge
> pycodestyle               2.5.0                    py37_0  
> pycosat                   0.6.3            py37h14c3975_0  
> pycparser                 2.19                     py37_0  
> pycrypto                  2.6.1            py37h14c3975_9  
> pycurl                    7.43.0.3         py37h1ba5d50_0  
> pyflakes                  2.1.1                    py37_0  
> pygments                  2.4.2                      py_0  
> pygpu                     0.7.6            py37h035aef0_0  
> pylint                    2.4.2                    py37_0  
> pyodbc                    4.0.27           py37he6710b0_0  
> pyopenssl                 19.0.0                   py37_0  
> pyparsing                 2.4.2                      py_0  
> pyqt                      5.9.2            py37h05f1152_2  
> pyrsistent                0.15.4           py37h7b6447c_0  
> pysocks                   1.7.1                    py37_0  
> pytables                  3.5.2            py37h71ec239_1  
> pytest                    5.2.1                    py37_0  
> pytest-arraydiff          0.3              py37h39e3cac_0  
> pytest-astropy            0.5.0                    py37_0  
> pytest-doctestplus        0.4.0                      py_0  
> pytest-openfiles          0.4.0                      py_0  
> pytest-remotedata         0.3.2                    py37_0  
> pytest-runner             5.2                        py_0  
> python                    3.7.4                h265db76_1  
> python-dateutil           2.8.0                    py37_0  
> python-libarchive-c       2.8                     py37_13  
> python-utils              2.3.0                    py37_0  
> pythreejs                 2.1.1                      py_0    conda-forge
> pytz                      2019.3                     py_0  
> pywavelets                1.0.3            py37hdd07704_1  
> pyyaml                    5.1.2            py37h7b6447c_0  
> pyzmq                     18.1.0           py37he6710b0_0  
> qt                        5.9.7                h5867ecd_1  
> qtawesome                 0.6.0                      py_0  
> qtconsole                 4.5.5                      py_0  
> qtpy                      1.9.0                      py_0  
> readline                  7.0                  h7b6447c_5  
> requests                  2.22.0                   py37_0  
> ripgrep                   0.10.0               hc07d326_0  
> rope                      0.14.0                     py_0  
> ruamel_yaml               0.15.46          py37h14c3975_0  
> s3fs                      0.2.0                    py37_0  
> s3transfer                0.2.1                    py37_0  
> scikit-image              0.15.0           py37he6710b0_0  
> scikit-learn              0.21.3           py37hd81dba3_0  
> scipy                     1.3.1            py37h7c811a0_0  
> seaborn                   0.9.0                    py37_0  
> secretstorage             3.1.1                    py37_0  
> send2trash                1.5.0                    py37_0  
> setuptools                41.4.0                   py37_0  
> simplegeneric             0.8.1                    py37_2  
> singledispatch            3.4.0.3                  py37_0  
> sip                       4.19.8           py37hf484d3e_0  
> six                       1.12.0                   py37_0  
> snappy                    1.1.7                hbae5bb6_3  
> snowballstemmer           2.0.0                      py_0  
> sortedcollections         1.1.2                    py37_0  
> sortedcontainers          2.1.0                    py37_0  
> soupsieve                 1.9.3                    py37_0  
> sphinx                    2.2.0                      py_0  
> sphinxcontrib             1.0                      py37_1  
> sphinxcontrib-applehelp   1.0.1                      py_0  
> sphinxcontrib-devhelp     1.0.1                      py_0  
> sphinxcontrib-htmlhelp    1.0.2                      py_0  
> sphinxcontrib-jsmath      1.0.1                      py_0  
> sphinxcontrib-qthelp      1.0.2                      py_0  
> sphinxcontrib-serializinghtml 1.1.3                      py_0  
> sphinxcontrib-websupport  1.1.2                      py_0  
> spyder                    3.3.6                    py37_0  
> spyder-kernels            0.5.2                    py37_0  
> sqlalchemy                1.3.9            py37h7b6447c_0  
> sqlite                    3.30.0               h7b6447c_0  
> statsmodels               0.10.1           py37hdd07704_0  
> sympy                     1.4                      py37_0  
> tabulate                  0.8.3                    py37_0  
> tbb                       2019.4               hfd86e86_0  
> tblib                     1.4.0                      py_0  
> tensorboard               2.0.0              pyhb38c66f_1  
> tensorflow                2.0.0           mkl_py37h66b46cc_0  
> tensorflow-base           2.0.0           mkl_py37h9204916_0  
> tensorflow-estimator      2.0.0              pyh2649769_0  
> termcolor                 1.1.0                    py37_1  
> terminado                 0.8.2                    py37_0  
> testpath                  0.4.2                    py37_0  
> theano                    1.0.4            py37hfd86e86_0  
> thrift-cpp                0.11.0               h02b749d_3  
> tk                        8.6.8                hbc83047_0  
> toolz                     0.10.0                     py_0  
> tornado                   6.0.3            py37h7b6447c_0  
> tqdm                      4.36.1                     py_0  
> traitlets                 4.3.3                    py37_0  
> traittypes                0.2.1                      py_1    conda-forge
> unicodecsv                0.14.1                   py37_0  
> unixodbc                  2.3.7                h14c3975_0  
> urllib3                   1.24.2                   py37_0  
> vaex                      2.5.0                      py_0    conda-forge
> vaex-arrow                0.4.2                      py_0    conda-forge
> vaex-astro                0.6.1                      py_1    conda-forge
> vaex-core                 1.4.0            py37hb3f55d8_0    conda-forge
> vaex-hdf5                 0.5.6                      py_0    conda-forge
> vaex-jupyter              0.4.1                      py_0    conda-forge
> vaex-ml                   0.7.0                      py_0    conda-forge
> vaex-server               0.2.1                      py_0    conda-forge
> vaex-viz                  0.3.8                      py_0    conda-forge
> wcwidth                   0.1.7                    py37_0  
> webencodings              0.5.1                    py37_1  
> werkzeug                  0.16.0                     py_0  
> wheel                     0.33.6                   py37_0  
> widgetsnbextension        3.5.1                    py37_0  
> wrapt                     1.11.2           py37h7b6447c_0  
> wurlitzer                 1.0.3                    py37_0  
> xarray                    0.14.1                     py_1  
> xlrd                      1.2.0                    py37_0  
> xlsxwriter                1.2.1                      py_0  
> xlwt                      1.3.0                    py37_0  
> xz                        5.2.4                h14c3975_4  
> yaml                      0.1.7                had09818_2  
> zeromq                    4.3.1                he6710b0_3  
> zict                      1.0.0                      py_0  
> zipp                      0.6.0                      py_0  
> zlib                      1.2.11               h7b6447c_3  
> zstd                      1.3.7                h0b5b093_0  
> 
>> Le 9 janv. 2020 à 15:03, Wes McKinney <wesmckinn@gmail.com <mailto:wesmckinn@gmail.com>>
a écrit :
>> 
>> hi,
>> 
>> Can you show the commands you used to install pyarrow? Please also
>> show the output of
>> 
>> conda list
>> 
>> It looks like you have conflicting library versions installed (for
>> example pyarrow or arrow-cpp from conda combined with pyarrow from
>> PyPI)
>> 
>> - Wes
>> 
>> On Thu, Jan 9, 2020 at 7:59 AM xxwang <xiaoni.wang@obspm.fr <mailto:xiaoni.wang@obspm.fr>>
wrote:
>>> 
>>> Dear all,
>>>    I removed my previous anaconda by rm ~/anaconda. Then I reinstalled the anaconda3
and packages (Pyarrow included). But I still got the errors:
>>> anaconda3/lib/python3.7/site-packages/pyarrow/lib.cpython-37m-x86_64-linux-gnu.so:
undefined symbol: _ZNK5arrow6Status8ToStringB5cxx11Ev
>>> 
>>> 
>>>    Thanks in advance !
>>> 
>>> Best regards
>>> 
>>> Xiaoni
>>> 
>>> Le 7 janv. 2020 à 16:04, Uwe L. Korn <uwelk@xhochy.com <mailto:uwelk@xhochy.com>>
a écrit :
>>> 
>>> Hello Xiaoni,
>>> 
>>> it seems that you have a conda environment and also installed pyarrow with conda
before. Mixing pip and conda installs of pyarrow is not going to work. Please recreate your
conda environment and install pyarrow from conda forge using "conda config --add channels
conda-forge && conda install pyarrow".
>>> 
>>> Cheers
>>> Uwe
>>> 
>>> On Tue, Jan 7, 2020, at 3:15 PM, xxwang wrote:
>>> 
>>> Dear all,
>>>     I tried to installed Pyarrow (within python 3.7), by using pip install pyarrow.
The installation seems OK. But when I do «  import pyarrow», then there is an error as below.
I do not understand why ….. If you could give some help, I will greatly appreciate !
>>> 
>>> Best regards
>>> Xiaoni
>>> 
>>> .conda/envs/python3/lib/python3.7/site-packages/pyarrow/lib.cpython-37m-x86_64-linux-gnu.so:
undefined symbol: _ZNK5arrow6Status8ToStringB5cxx11Ev
>>> 
>>> 
> 


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