ValueError: module functions cannot set METH_CLASS or METH_STATIC

[joh]

Code Sample, a copy-pastable example if possible

import matplotlib.pyplot as plt
import pandas as pd

Problem description

If I import pyplot before pandas, I get the following error:

Traceback (most recent call last):
  File "bug_pandas.py", line 2, in <module>
    import pandas as pd
  File "/home/joh/.local/lib/python3.6/site-packages/pandas/__init__.py", line 57, in <module>
    from pandas.io.api import *
  File "/home/joh/.local/lib/python3.6/site-packages/pandas/io/api.py", line 19, in <module>
    from pandas.io.packers import read_msgpack, to_msgpack
  File "/home/joh/.local/lib/python3.6/site-packages/pandas/io/packers.py", line 69, in <module>
    from pandas.util._move import (
ValueError: module functions cannot set METH_CLASS or METH_STATIC

If I re-order the imports so that pandas is imported first, the error disappears. Not sure if this is an issue with pyplot or pandas, but the exception seems to come from within pandas.

Expected Output

Output of pd.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.6.6.final.0 python-bits: 64 OS: Linux OS-release: 4.18.8-041808-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: en_US.UTF-8 LANG: en_US.UTF-8 LOCALE: en_US.UTF-8

pandas: 0.23.4
pytest: 3.8.0
pip: 9.0.1
setuptools: 40.4.3
Cython: None
numpy: 1.15.2
scipy: 0.19.1
pyarrow: None
xarray: None
IPython: 5.5.0
sphinx: 1.6.7
patsy: None
dateutil: 2.7.3
pytz: 2018.5
blosc: None
bottleneck: 1.2.0
tables: 3.4.2
numexpr: 2.6.4
feather: None
matplotlib: 2.1.1
openpyxl: 2.4.9
xlrd: 1.1.0
xlwt: None
xlsxwriter: None
lxml: 4.2.1
bs4: 4.6.0
html5lib: 0.999999999
sqlalchemy: 1.1.11
pymysql: None
psycopg2: None
jinja2: 2.10
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None

[pambot]

@joh I personally could not reproduce this bug, but digging into my pd.show_versions(), it looks like I'm on matplotlib: 3.0.0 and you're on 2.1.1. Could you try updating your environment to the latest versions? It may be just an unfortunate misalignment due to a major version change.

[TomAugspurger]

I'm also not able to reproduce.

@joh how did you install pandas and matplotlib?

[joh]

I upgraded matplotlib to 3.0.0 via pip:

INSTALLED VERSIONS ------------------ commit: None python: 3.6.6.final.0 python-bits: 64 OS: Linux OS-release: 4.18.8-041808-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: en_US.UTF-8 LANG: en_US.UTF-8 LOCALE: en_US.UTF-8

pandas: 0.23.4
pytest: 3.8.0
pip: 9.0.1
setuptools: 40.4.3
Cython: None
numpy: 1.15.2
scipy: 0.19.1
pyarrow: None
xarray: None
IPython: 5.5.0
sphinx: 1.6.7
patsy: None
dateutil: 2.7.3
pytz: 2018.5
blosc: None
bottleneck: 1.2.0
tables: 3.4.2
numexpr: 2.6.4
feather: None
matplotlib: 3.0.0
openpyxl: 2.4.9
xlrd: 1.1.0
xlwt: None
xlsxwriter: None
lxml: 4.2.1
bs4: 4.6.0
html5lib: 0.999999999
sqlalchemy: 1.1.11
pymysql: None
psycopg2: None
jinja2: 2.10
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None

I still get the same error:

$ python3 -c 'import matplotlib.pyplot as plt; import pandas as pd'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/joh/.local/lib/python3.6/site-packages/pandas/__init__.py", line 57, in <module>
    from pandas.io.api import *
  File "/home/joh/.local/lib/python3.6/site-packages/pandas/io/api.py", line 19, in <module>
    from pandas.io.packers import read_msgpack, to_msgpack
  File "/home/joh/.local/lib/python3.6/site-packages/pandas/io/packers.py", line 69, in <module>
    from pandas.util._move import (
ValueError: module functions cannot set METH_CLASS or METH_STATIC

@TomAugspurger I installed both pandas and matplotlib through pip.

[TomAugspurger]

@joh do you have the install log? Or can you reinstall pandas and matplotlib in a virtualenv and post the output? Something is going wrong with that C file.

[joh]

@TomAugspurger I installed pandas and matplotlib in a virtualenv and discovered that I only get the error if matplotlib is configured to use the GTK3Agg or GTK3Cairo backend.

[TomAugspurger]

Ah, hmm. This is beginning to sound like #19706 but with a different error message.

None of the pandas or matplotlib devs are able to reproduce it :/

[Dominnio]

I get the same error :

Traceback (most recent call last):
  File "start.py", line 20, in <module>
    import FlowCal
  File "/home/dominik/.local/lib/python3.6/site-packages/FlowCal/__init__.py", line 12, in <module>
    from . import excel_ui
  File "/home/dominik/.local/lib/python3.6/site-packages/FlowCal/excel_ui.py", line 98, in <module>
    import pandas as pd
  File "/home/dominik/.local/lib/python3.6/site-packages/pandas/__init__.py", line 57, in <module>
    from pandas.io.api import *
  File "/home/dominik/.local/lib/python3.6/site-packages/pandas/io/api.py", line 19, in <module>
    from pandas.io.packers import read_msgpack, to_msgpack
  File "/home/dominik/.local/lib/python3.6/site-packages/pandas/io/packers.py", line 69, in <module>
    from pandas.util._move import (
ValueError: module functions cannot set METH_CLASS or METH_STATIC

But when I change import order then the error doesn't occur.

[TomAugspurger]

Any debugging you can do would be appreciated.

…

On Sun, Oct 14, 2018 at 2:02 PM Dominik Orliński ***@***.***> wrote: I get the same error : Traceback (most recent call last): File "start.py", line 20, in <module> import FlowCal File "/home/dominik/.local/lib/python3.6/site-packages/FlowCal/__init__.py", line 12, in <module> from . import excel_ui File "/home/dominik/.local/lib/python3.6/site-packages/FlowCal/excel_ui.py", line 98, in <module> import pandas as pd File "/home/dominik/.local/lib/python3.6/site-packages/pandas/__init__.py", line 57, in <module> from pandas.io.api import * File "/home/dominik/.local/lib/python3.6/site-packages/pandas/io/api.py", line 19, in <module> from pandas.io.packers import read_msgpack, to_msgpack File "/home/dominik/.local/lib/python3.6/site-packages/pandas/io/packers.py", line 69, in <module> from pandas.util._move import ( ValueError: module functions cannot set METH_CLASS or METH_STATIC But when I change import order then the error doesn't occur. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#23040 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABQHIqh1GPMr_nhAAiBEY4QQ5TLlJKE0ks5uk4o8gaJpZM4XMa4h> .

[AlfTang]

Got same error as well:

Traceback (most recent call last):
  File "/home/user/apiservices/apiservices/urls.py", line 19, in <module>
    from patentClustering import views
  File "/home/user/apiservices/patentClustering/views.py", line 12, in <module>
    import pandas as pd
  File "/usr/local/lib/python3.6/dist-packages/pandas/__init__.py", line 57, in <module>
    from pandas.io.api import *
  File "/usr/local/lib/python3.6/dist-packages/pandas/io/api.py", line 19, in <module>
    from pandas.io.packers import read_msgpack, to_msgpack
  File "/usr/local/lib/python3.6/dist-packages/pandas/io/packers.py", line 69, in <module>
    from pandas.util._move import (
ValueError: module functions cannot set METH_CLASS or METH_STATIC

The problem is fixed it by changing pandas import order as suggested. I suspect that the cause is python3.6. When I used python 3.5.2 everything worked fine.

[lazka]

I've reduced this down to:

import ctypes
ctypes.CDLL("libgtk-3.so.0", ctypes.RTLD_GLOBAL)
import pandas

This loads libatk-bridge-2.0.so, containing:

0000000000033300 g    DO .data  0000000000000070  Base        methods

which conflicts with

pandas/pandas/util/move.c

Line 188 in 9f2c716

PyMethodDef methods[] = {

Presumably internal linkage should be used in both cases.

EDIT: I opened marge request for at-spi2-atk: https://gitlab.gnome.org/GNOME/at-spi2-atk/merge_requests/2.