Import Error with version 1.6.0

[atremblay]

Created a new env with conda

conda create -n spacy python=3.5 ipython

and then install spacy (1.6.0) with pip (conda still has version 0.101.0)

pip install spacy

But I still get this error.

In [1]: import spacy
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-c080f6458562> in <module>()
----> 1 import spacy

/home/alexis/anaconda3/envs/spacy/lib/python3.5/site-packages/spacy/__init__.py in <module>()
      4 from .about import __version__
      5
----> 6 from . import en
      7 from . import de
      8 from . import zh

/home/alexis/anaconda3/envs/spacy/lib/python3.5/site-packages/spacy/en/__init__.py in <module>()
      6 from ..util import match_best_version
      7 from ..util import get_data_path
----> 8 from ..language import Language
      9 from ..lemmatizer import Lemmatizer
     10 from ..vocab import Vocab

/home/alexis/anaconda3/envs/spacy/lib/python3.5/site-packages/spacy/language.py in <module>()
     15
     16
---> 17 from .tokenizer import Tokenizer
     18 from .vocab import Vocab
     19 from .tagger import Tagger

ImportError: /home/alexis/anaconda3/envs/spacy/lib/python3.5/site-packages/spacy/tokenizer.cpython-35m-x86_64-linux-gnu.so: undefined symbol: _ZTINSt8ios_base7failureB5cxx11E

There is a similar issue here explosion/sense2vec#19 but that solution did not help.

Note, I don't have that problem on MacOS Sierra.

Environment

• Operating System: Ubuntu 16.04.1 LTS

 % conda list
# packages in environment at /home/alexis/anaconda3/envs/spacy:
#
cloog                     0.18.0                        0
cloudpickle               0.2.2                     <pip>
cymem                     1.31.2                    <pip>
cytoolz                   0.8.2                     <pip>
decorator                 4.0.11                   py35_0
flexmock                  0.10.2                    <pip>
gmp                       6.1.0                         0
ipython                   5.2.2                    py35_0
ipython_genutils          0.1.0                    py35_0
isl                       0.15                          0
libgcc                    5.2.0                         0
mpc                       1.0.3                         0
mpfr                      3.1.5                         0
murmurhash                0.26.4                    <pip>
numpy                     1.12.0                    <pip>
openssl                   1.0.2k                        0
path.py                   10.1                     py35_0
pathlib                   1.0.1                     <pip>
pexpect                   4.2.1                    py35_0
pickleshare               0.7.4                    py35_0
pip                       9.0.1                    py35_1
plac                      0.9.6                     <pip>
preshed                   0.46.4                    <pip>
prompt_toolkit            1.0.9                    py35_0
ptyprocess                0.5.1                    py35_0
pygments                  2.1.3                    py35_0
python                    3.5.2                         0
readline                  6.2                           2
semver                    2.7.5                     <pip>
setuptools                27.2.0                   py35_0
simplegeneric             0.8.1                    py35_1
six                       1.10.0                   py35_0
spacy                     1.6.0                     <pip>
sputnik                   0.9.3                     <pip>
sqlite                    3.13.0                        0
thinc                     6.2.0                     <pip>
tk                        8.5.18                        0
toolz                     0.8.2                     <pip>
tqdm                      4.11.2                    <pip>
traitlets                 4.3.1                    py35_0
ujson                     1.35                      <pip>
wcwidth                   0.1.7                    py35_0
wheel                     0.29.0                   py35_0
xz                        5.2.2                         1
zlib                      1.2.8                         3

[honnibal]

Most of the time this sort of error comes down to the PATH ordering leading to an unexpected copy of pip being executed. Could you do:

pip --version

And

python -m pip --version

To check that when you do pip install spacy, the copy of pip that's being run is what you expect?

If problems persist, the more manual process --- that therefore gives you more control --- is to clone the repository and compile the code using python setup.py build_ext --inplace. You can then do python setup.py sdist to create the distribution file, which you can intall using pip. This gives you end-to-end control of the build, so if something goes wrong you can see what's going on.

[atremblay]

pip --version did output the one from my conda env.

Just in case I created a new one with everything

conda create -n spacy python=3.5 anaconda

I then proceeded to follow your steps and as far as I can tell it seemed to be alright. Building took a long time and there were a lot of outputs. Cannot really print it here. Unfortunately in the end I still get the same error.

Here is the full list of packages that were installed

±% conda list
# packages in environment at /home/alexis/anaconda3/envs/spacy:
#
_license                  1.1                      py35_1
alabaster                 0.7.9                    py35_0
anaconda                  4.3.0               np111py35_0
anaconda-client           1.6.0                    py35_0
anaconda-navigator        1.4.3                    py35_0
argcomplete               1.0.0                    py35_1
astroid                   1.4.9                    py35_0
astropy                   1.3                 np111py35_0
babel                     2.3.4                    py35_0
backports                 1.0                      py35_0
beautifulsoup4            4.5.3                    py35_0
bitarray                  0.8.1                    py35_0
blaze                     0.10.1                   py35_0
bokeh                     0.12.4                   py35_0
boto                      2.45.0                   py35_0
bottleneck                1.2.0               np111py35_0
cairo                     1.14.8                        0
cffi                      1.9.1                    py35_0
chardet                   2.3.0                    py35_0
chest                     0.2.3                    py35_0
click                     6.7                      py35_0
cloudpickle               0.2.2                    py35_0
clyent                    1.2.2                    py35_0
colorama                  0.3.7                    py35_0
configobj                 5.0.6                    py35_0
contextlib2               0.5.4                    py35_0
cryptography              1.7.1                    py35_0
curl                      7.52.1                        0
cycler                    0.10.0                   py35_0
cymem                     1.31.2                    <pip>
cython                    0.25.2                   py35_0
cytoolz                   0.8.2                    py35_0
dask                      0.13.0                   py35_0
datashape                 0.5.4                    py35_0
dbus                      1.10.10                       0
decorator                 4.0.11                   py35_0
dill                      0.2.5                    py35_0
docutils                  0.13.1                   py35_0
entrypoints               0.2.2                    py35_0
et_xmlfile                1.0.1                    py35_0
expat                     2.1.0                         0
fastcache                 1.0.2                    py35_1
flask                     0.12                     py35_0
flask-cors                3.0.2                    py35_0
flexmock                  0.10.2                    <pip>
fontconfig                2.12.1                        2
freetype                  2.5.5                         2
get_terminal_size         1.0.0                    py35_0
gevent                    1.2.1                    py35_0
glib                      2.50.2                        1
greenlet                  0.4.11                   py35_0
gst-plugins-base          1.8.0                         0
gstreamer                 1.8.0                         0
h5py                      2.6.0               np111py35_2
harfbuzz                  0.9.39                        2
hdf5                      1.8.17                        1
heapdict                  1.0.0                    py35_1
icu                       54.1                          0
idna                      2.2                      py35_0
imagesize                 0.7.1                    py35_0
ipykernel                 4.5.2                    py35_0
ipython                   5.1.0                    py35_0
ipython_genutils          0.1.0                    py35_0
ipywidgets                5.2.2                    py35_1
isort                     4.2.5                    py35_0
itsdangerous              0.24                     py35_0
jbig                      2.1                           0
jdcal                     1.3                      py35_0
jedi                      0.9.0                    py35_1
jinja2                    2.9.4                    py35_0
jpeg                      9b                            0
jsonschema                2.5.1                    py35_0
jupyter                   1.0.0                    py35_3
jupyter_client            4.4.0                    py35_0
jupyter_console           5.0.0                    py35_0
jupyter_core              4.2.1                    py35_0
lazy-object-proxy         1.2.2                    py35_0
libffi                    3.2.1                         1
libgcc                    4.8.5                         2
libgfortran               3.0.0                         1
libiconv                  1.14                          0
libpng                    1.6.27                        0
libsodium                 1.0.10                        0
libtiff                   4.0.6                         3
libxcb                    1.12                          1
libxml2                   2.9.4                         0
libxslt                   1.1.29                        0
llvmlite                  0.15.0                   py35_0
locket                    0.2.0                    py35_1
lxml                      3.7.2                    py35_0
markupsafe                0.23                     py35_2
matplotlib                2.0.0               np111py35_0
mistune                   0.7.3                    py35_0
mkl                       2017.0.1                      0
mkl-service               1.1.2                    py35_3
mpmath                    0.19                     py35_1
multipledispatch          0.4.9                    py35_0
murmurhash                0.26.4                    <pip>
nbconvert                 4.2.0                    py35_0
nbformat                  4.2.0                    py35_0
networkx                  1.11                     py35_0
nltk                      3.2.2                    py35_0
nose                      1.3.7                    py35_1
notebook                  4.3.1                    py35_0
numba                     0.30.1              np111py35_0
numexpr                   2.6.1               np111py35_2
numpy                     1.11.3                   py35_0
numpydoc                  0.6.0                    py35_0
odo                       0.5.0                    py35_1
openpyxl                  2.4.1                    py35_0
openssl                   1.0.2k                        0
pandas                    0.19.2              np111py35_1
partd                     0.3.7                    py35_0
path.py                   10.0                     py35_0
pathlib                   1.0.1                     <pip>
pathlib2                  2.2.0                    py35_0
patsy                     0.4.1                    py35_0
pcre                      8.39                          1
pep8                      1.7.0                    py35_0
pexpect                   4.2.1                    py35_0
pickleshare               0.7.4                    py35_0
pillow                    4.0.0                    py35_0
pip                       9.0.1                    py35_1
pixman                    0.34.0                        0
plac                      0.9.2                     <pip>
ply                       3.9                      py35_0
preshed                   0.46.4                    <pip>
prompt_toolkit            1.0.9                    py35_0
psutil                    5.0.1                    py35_0
ptyprocess                0.5.1                    py35_0
py                        1.4.32                   py35_0
pyasn1                    0.1.9                    py35_0
pycosat                   0.6.1                    py35_1
pycparser                 2.17                     py35_0
pycrypto                  2.6.1                    py35_4
pycurl                    7.43.0                   py35_2
pyflakes                  1.5.0                    py35_0
pygments                  2.1.3                    py35_0
pylint                    1.6.4                    py35_1
pyopenssl                 16.2.0                   py35_0
pyparsing                 2.1.4                    py35_0
pyqt                      5.6.0                    py35_2
pytables                  3.3.0               np111py35_0
pytest                    3.0.5                    py35_0
python                    3.5.2                         0
python-dateutil           2.6.0                    py35_0
pytz                      2016.10                  py35_0
pyyaml                    3.12                     py35_0
pyzmq                     16.0.2                   py35_0
qt                        5.6.2                         3
qtawesome                 0.4.3                    py35_0
qtconsole                 4.2.1                    py35_1
qtpy                      1.2.1                    py35_0
readline                  6.2                           2
redis                     3.2.0                         0
redis-py                  2.10.5                   py35_0
requests                  2.12.4                   py35_0
rope                      0.9.4                    py35_1
scikit-image              0.12.3              np111py35_1
scikit-learn              0.18.1              np111py35_1
scipy                     0.18.1              np111py35_1
seaborn                   0.7.1                    py35_0
semver                    2.7.5                     <pip>
setuptools                27.2.0                   py35_0
simplegeneric             0.8.1                    py35_1
singledispatch            3.4.0.3                  py35_0
sip                       4.18                     py35_0
six                       1.10.0                   py35_0
snowballstemmer           1.2.1                    py35_0
sockjs-tornado            1.0.3                    py35_0
spacy                     1.6.0                     <pip>
sphinx                    1.5.1                    py35_0
sputnik                   0.9.3                     <pip>
spyder                    3.1.2                    py35_0
sqlalchemy                1.1.5                    py35_0
sqlite                    3.13.0                        0
statsmodels               0.6.1               np111py35_1
sympy                     1.0                      py35_0
terminado                 0.6                      py35_0
thinc                     6.2.0                     <pip>
tk                        8.5.18                        0
toolz                     0.8.2                    py35_0
tornado                   4.4.2                    py35_0
tqdm                      4.11.2                    <pip>
traitlets                 4.3.1                    py35_0
ujson                     1.35                      <pip>
unicodecsv                0.14.1                   py35_0
wcwidth                   0.1.7                    py35_0
werkzeug                  0.11.15                  py35_0
wheel                     0.29.0                   py35_0
widgetsnbextension        1.2.6                    py35_0
wrapt                     1.10.8                   py35_0
xlrd                      1.0.0                    py35_0
xlsxwriter                0.9.6                    py35_0
xlwt                      1.2.0                    py35_0
xz                        5.2.2                         1
yaml                      0.1.6                         0
zeromq                    4.1.5                         0
zlib                      1.2.8                         3

[rmax]

The conda-forge channel now has spaCy packages up to the latest release. You can install them via: conda install -c conda-forge spacy

[the-holger]

I'm facing the same problem on MacOS Sierra with a new Miniconda installation.

My error message is a tad different though and might be more helpful:

from .tokenizer import Tokenizer
File ".env/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd", line 155, in init spacy.tokenizer (spacy/tokenizer.cpp:12130)
File "/Users/holger/miniconda3/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module>

Ending in:

 AttributeError: module 'threading' has no attribute 'RLock'

I have positively no clue where the
.env/local/lib/python2.7/site-packages/Cython/Includes/numpy/
import path come from. No Python 2.7 installed and no .env directory there either.

[atremblay]

Thanks @rolando installing with conda-forge solves the problem. Still don't know what's happening exactly. conda-forge installs these

(spacy) glitch@gpu-instance:~$ conda install spacy -c conda-forge
Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/glitch/anaconda3/envs/spacy:

The following NEW packages will be INSTALLED:

    cymem:      1.31.2-py35_0     conda-forge
    murmurhash: 0.26.4-py35_0     conda-forge
    plac:       0.9.6-py35_0
    preshed:    0.46.4-py35_0     conda-forge
    semver:     2.7.5-py35_0      conda-forge
    spacy:      1.6.0-np111py35_0 conda-forge
    sputnik:    0.9.3-py35_0      conda-forge
    thinc:      6.2.0-np111py35_0 conda-forge
    tqdm:       4.11.2-py35_0     conda-forge
    ujson:      1.35-py35_0

and pip installs

(spacy) glitch@gpu-instance:~$ pip install spacy
Collecting spacy
Collecting preshed<0.47.0,>=0.46.0 (from spacy)
Requirement already satisfied: six in ./anaconda3/envs/spacy/lib/python3.6/site-packages (from spacy)
Requirement already satisfied: cloudpickle in ./anaconda3/envs/spacy/lib/python3.6/site-packages (from spacy)
Collecting plac (from spacy)
  Using cached plac-0.9.6-py2.py3-none-any.whl
Collecting cymem<1.32,>=1.30 (from spacy)
Collecting thinc<6.3.0,>=6.2.0 (from spacy)
Collecting ujson>=1.35 (from spacy)
Collecting sputnik<0.10.0,>=0.9.2 (from spacy)
  Using cached sputnik-0.9.3-py2.py3-none-any.whl
Collecting murmurhash<0.27,>=0.26 (from spacy)
Requirement already satisfied: numpy>=1.7 in ./anaconda3/envs/spacy/lib/python3.6/site-packages (from spacy)
Collecting pathlib (from spacy)
Requirement already satisfied: cytoolz<0.9,>=0.8 in ./anaconda3/envs/spacy/lib/python3.6/site-packages (from thinc<6.3.0,>=6.2.0->spacy)
Collecting tqdm<5.0.0,>=4.10.0 (from thinc<6.3.0,>=6.2.0->spacy)
  Using cached tqdm-4.11.2-py2.py3-none-any.whl
Collecting flexmock (from thinc<6.3.0,>=6.2.0->spacy)
Collecting semver (from sputnik<0.10.0,>=0.9.2->spacy)
Installing collected packages: cymem, preshed, plac, tqdm, murmurhash, flexmock, thinc, ujson, semver, sputnik, pathlib, spacy
Successfully installed cymem-1.31.2 flexmock-0.10.2 murmurhash-0.26.4 pathlib-1.0.1 plac-0.9.6 preshed-0.46.4 semver-2.7.6 spacy-1.6.0 sputnik-0.9.3 thinc-6.2.0 tqdm-4.11.2 ujson-1.35

It's a spot the difference game. In both cases I removed the spacy env and recreated it with
conda create -n spacy python=3.5 anaconda

Hope this helps.

P.S.: In case you're wondering, I created a new account on the server just in case. That's why the user was alexis and now it's glitch

[honnibal]

Thanks for updating 🎉

[lock]

This thread has been automatically locked since there has not been any recent activity after it was closed. Please open a new issue for related bugs.