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conda-forge / pyarrow-feedstock

A conda-smithy repository for pyarrow.
BSD 3-Clause "New" or "Revised" License
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ImportError: undefined symbol #58

Closed gwerbin closed 5 years ago

gwerbin commented 5 years ago

Issue: ImportError: undefined symbol

Not sure if it's an Arrow issue or a Conda one. Or (more likely) just something broken in my environment.

I had pyarrow 0.11 installed at first. Downgrading to 0.10 and 0.9 didn't fix the problem.

import pyarrow.parquet as pq
# Traceback (most recent call last):
#   File "<stdin>", line 1, in <module>
#   File "/<redacted>/projects/<redacted>/conda-env/lib/python3.6/site-packages/pyarrow/__init__.py", line 47, in <module>
#     from pyarrow.lib import cpu_count, set_cpu_count
# ImportError: /<redacted>/projects/<redacted>/conda-env/lib/python3.6/site-packages/pyarrow/../../../libarrow.so.0: undefined symbol: _ZN5boost13match_resultsIN9__gnu_cxx17__normal_iteratorIPKcSsEESaINS_9sub_matchIS5_EEEE12maybe_assignERKS9_


Environment (conda list):

``` # packages in environment at /opt/app/data/home_extenstion/gregory-werbin/projects/tts-classification/conda-env: # # Name Version Build Channel _py-xgboost-mutex 2.0 cpu_0 appdirs 1.4.3 arrow-cpp 0.9.0 py36h70250a7_7 conda-forge asn1crypto 0.24.0 py36_0 atomicwrites 1.2.1 py_0 conda-forge attrs 18.2.0 py_0 conda-forge backcall 0.1.0 py36_0 bidict 0.17.3 py_0 conda-forge blas 1.0 mkl boost-cpp 1.67.0 h14c3975_4 boto 2.49.0 py36_0 boto3 1.9.21 py36_0 botocore 1.12.23 py36_0 bz2file 0.98 bzip2 1.0.6 h14c3975_5 ca-certificates 2018.10.15 ha4d7672_0 conda-forge category_encoders 1.3.0 py_0 conda-forge certifi 2018.10.15 py36_1000 conda-forge cffi 1.11.5 py36he75722e_1 chardet 3.0.4 py36_1 ConfigArgParse 0.13.0 cryptography 2.3.1 py36hc365091_0 cycler 0.10.0 py36_0 cymem 2.0.2 py36hfd86e86_0 cytoolz 0.9.0.1 py36h14c3975_1 datrie 0.7.1 dbus 1.13.2 h714fa37_1 decorator 4.3.0 py36_0 dill 0.2.8.2 py36_0 docutils 0.14 py36_0 expat 2.2.6 he6710b0_0 fastparquet 0.1.6 py36_0 conda-forge fasttext 0.1.0 hfc679d8_0 conda-forge fontconfig 2.13.0 h9420a91_0 freetype 2.9.1 h8a8886c_1 gensim 3.6.0 gitdb2 2.0.5 GitPython 2.1.11 glib 2.56.2 hd408876_0 gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb453b48_1 icu 58.2 h9c2bf20_1 idna 2.7 py36_0 imbalanced-learn 0.4.1 py_0 conda-forge intel-openmp 2019.0 118 ipykernel 5.1.0 py36h39e3cac_0 ipython 7.0.1 py36h39e3cac_0 ipython_genutils 0.2.0 py36_0 jedi 0.13.1 py36_0 jmespath 0.9.3 py36_0 jpeg 9b h024ee3a_2 jsonschema 2.6.0 jupyter_client 5.2.3 py36_0 jupyter_core 4.4.0 py36_0 kiwisolver 1.0.1 py36hf484d3e_0 libboost 1.67.0 h46d08c1_4 libedit 3.1.20170329 h6b74fdf_2 libffi 3.2.1 hd88cf55_4 libgcc-ng 8.2.0 hdf63c60_1 libgfortran-ng 7.3.0 hdf63c60_0 libpng 1.6.35 hbc83047_0 libsodium 1.0.16 h1bed415_0 libstdcxx-ng 8.2.0 hdf63c60_1 libuuid 1.0.3 h1bed415_2 libxcb 1.13 h1bed415_1 libxgboost 0.80 hfc679d8_1 conda-forge libxml2 2.9.8 h26e45fe_1 lightgbm 2.2.1 py36hfc679d8_0 conda-forge llvmlite 0.25.0 py36hd28b015_1 conda-forge matplotlib 3.0.0 py36h5429711_0 mkl 2019.0 118 mkl_fft 1.0.6 py36h7dd41cf_0 mkl_random 1.0.1 py36h4414c95_1 more-itertools 4.3.0 py36_1000 conda-forge msgpack-numpy 0.4.3.2 py36_0 msgpack-python 0.5.6 py36h6bb024c_1 murmurhash 1.0.1 py36he6710b0_0 ncurses 6.1 hf484d3e_0 nltk 3.3.0 py36_0 numba 0.40.0 py36hf8a1672_0 conda-forge numpy 1.15.2 py36h1d66e8a_1 numpy-base 1.15.2 py36h81de0dd_1 openssl 1.0.2p h470a237_1 conda-forge pandas 0.23.4 py36h04863e7_0 parquet-cpp 1.4.0 h83d4a3d_2 conda-forge parso 0.3.1 py36_0 patsy 0.5.0 py36_0 pcre 8.42 h439df22_0 pexpect 4.6.0 py36_0 pickleshare 0.7.5 py36_0 pip 10.0.1 py36_0 plac 0.9.6 py36_0 pluggy 0.8.0 py_0 conda-forge preshed 2.0.1 py36he6710b0_0 prompt_toolkit 2.0.6 py36_0 ptyprocess 0.6.0 py36_0 py 1.7.0 py_0 conda-forge py-xgboost 0.80 py36hfc679d8_1 conda-forge pyarrow 0.9.0 py36hfc679d8_2 conda-forge pycparser 2.19 py36_0 pygments 2.2.0 py36_0 pyopenssl 18.0.0 py36_0 pyparsing 2.2.2 py36_0 pyqt 5.9.2 py36h05f1152_2 pysocks 1.6.8 py36_0 pytest 3.9.1 py36_1000 conda-forge python 3.6.6 h6e4f718_2 python-dateutil 2.7.3 py36_0 pytz 2018.5 py36_0 PyYAML 3.13 pyzmq 17.1.2 py36h14c3975_0 qt 5.9.6 h8703b6f_2 ratelimiter 1.2.0.post0 readline 7.0 h7b6447c_5 regex 2018.08.29 py36h7b6447c_0 requests 2.19.1 py36_0 s3transfer 0.1.13 py36_0 scikit-learn 0.20.0 py36h4989274_1 scipy 1.1.0 py36hfa4b5c9_1 setuptools 40.4.3 py36_0 simplegeneric 0.8.1 py36_2 sip 4.19.8 py36hf484d3e_0 six 1.11.0 py36_1 smart_open 1.7.1 py36_0 smmap2 2.0.5 snakemake 5.3.0 spacy 2.0.16 py36h962f231_0 sqlite 3.25.2 h7b6447c_0 statsmodels 0.9.0 py36h035aef0_0 thinc 6.12.0 py36h4989274_0 thrift 0.11.0 py36hfc679d8_1 conda-forge tk 8.6.8 hbc83047_0 toolz 0.9.0 py36_0 tornado 5.1.1 py36h7b6447c_0 tqdm 4.27.0 pyha03479a_0 traitlets 4.3.2 py36_0 ujson 1.35 py36h14c3975_0 urllib3 1.23 py36_0 wcwidth 0.1.7 py36_0 wheel 0.32.1 py36_0 wrapt 1.10.11 py36h14c3975_2 xlrd 1.1.0 py36_1 xz 5.2.4 h14c3975_4 zeromq 4.2.5 hf484d3e_1 zlib 1.2.11 ha838bed_2 ```


Details about conda and system ( conda info ):

``` active environment : //projects//conda-env active env location : //projects//conda-env shell level : 1 user config file : //.condarc populated config files : //.condarc conda version : 4.5.0 conda-build version : 3.0.31 python version : 3.6.1.final.0 base environment : //anaconda3 (read only) channel URLs : /linux-64 /noarch https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /opt/app/anaconda3/pkgs //.conda/pkgs envs directories : //.conda/envs //envs platform : linux-64 user-agent : conda/4.5.0 requests/2.18.4 CPython/3.6.1 Linux/3.10.0-514.26.2.el7.x86_64 rhel/7.3 glibc/2.17 UID:GID : 51757:51714 netrc file : None offline mode : False ```
wesm commented 5 years ago

Try uninstalling libboost

spk83 commented 5 years ago

Getting similar error and uninstalling libboost fixed it. but this may be the root cause here? https://github.com/ContinuumIO/anaconda-issues/issues/9287

xhochy commented 5 years ago

Uninstalling libboost is the correct option here. Don't mix packages from defaults and conda-forge.