ValueError: module functions cannot set METH_CLASS or METH_STATIC #23040

joh · 2018-10-08T08:01:26Z

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

The text was updated successfully, but these errors were encountered:

pambot · 2018-10-08T17:43:33Z

@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 · 2018-10-08T18:05:44Z

I'm also not able to reproduce.

@joh how did you install pandas and matplotlib?

joh · 2018-10-10T07:48:10Z

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 · 2018-10-10T11:09:12Z

@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 · 2018-10-10T13:30:10Z

@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 · 2018-10-10T13:35:15Z

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 · 2018-10-14T19:02:11Z

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 · 2018-10-14T19:04:21Z

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> .

…s-dev#19706) There appears to be symbol collisions with matplotlib in `pandas/util/move.c`. Make symbols that are not intended to be exported static, so they are neither exported nor dynamically resolved.

AlfTang · 2018-11-08T08:15:49Z

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 · 2018-12-05T15:37:27Z

I've reduced this down to:

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

ghost · 2018-12-05T16:20:08Z

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.

TomAugspurger · 2018-12-06T21:12:23Z

Hopefully fixed by #24113.

…rary If pandas is imported after some other libraries, the operation fails https://askubuntu.com/questions/1081651/failing-to-import-pandas-in-anjuta-module-functions-cannot-set-meth-class-or-me pandas-dev/pandas#23040

TheChymera · 2019-03-04T21:46:24Z

I recently encountered this error after a system update (pandas itself was not updated, but other things were). It was fixed by moving to a post-0.24 version, but this clashes with another great library I use, statsmodels, which has not yet fully migrated to the API updates.

Since it was neither a pandas nor a statsmodels update which lead to this issue materializing on my system, I was wondering if perhaps you have any advice regarding what else I could try to temporarily downgrade.

lazka · 2019-03-05T10:15:47Z

At least for this specific problem the other package is libatk-bridge2.0-0 on Ubuntu. On other distros the package containing libatk-bridge-2.0.so.0.0.0

slaweksiluk · 2019-03-07T10:06:35Z

sudo -H pip3 uninstall matplotlib
sudo -H apt-get install python3-matplotlib

Fixed ValueError and other warnings on my Ubuntu18.

dstreppa · 2019-11-13T16:42:11Z

I've experienced today a similar problem, below the traceback:

Traceback (most recent call last):
  File "/home/bombolo/PycharmProjects/mulder-algo/mulder_algo/run_mulder.py", line 6, in 
    from mulder_algo.agent_aggregator import AgentAggregator
  File "/home/bombolo/PycharmProjects/mulder-algo/mulder_algo/agent_aggregator.py", line 7, in 
    from optisim.utils import InputDataManager
  File "/home/bombolo/PycharmProjects/optisim/optisim/__init__.py", line 2, in 
    from . import agents
  File "/home/bombolo/PycharmProjects/optisim/optisim/agents/__init__.py", line 2, in 
    from . import boiler
  File "/home/bombolo/PycharmProjects/optisim/optisim/agents/boiler.py", line 9, in 
    from .heat_pump import HeatPump
  File "/home/bombolo/PycharmProjects/optisim/optisim/agents/heat_pump.py", line 4, in 
    import pandas as pd
  File "/home/bombolo/PycharmProjects/optisim/venv/lib/python3.6/site-packages/pandas/__init__.py", line 57, in 
    from pandas.io.api import *
  File "/home/bombolo/PycharmProjects/optisim/venv/lib/python3.6/site-packages/pandas/io/api.py", line 19, in 
    from pandas.io.packers import read_msgpack, to_msgpack
  File "/home/bombolo/PycharmProjects/optisim/venv/lib/python3.6/site-packages/pandas/io/packers.py", line 69, in 
    from pandas.util._move import (
ValueError: module functions cannot set METH_CLASS or METH_STATIC

After a hour of fighting I solved the problem creating a new venv based on Python3.6.8 (before it was 3.6.7-based). I hope this can help.

vigkrish92 · 2019-12-17T18:18:04Z

import pandas as pd
import matplotlib.pyplot as plt

I have faced the same error, I re-arranged the import order. It was working fine for me. Thanks

masaduzz1 · 2020-06-29T16:31:56Z

import pandas as pd
import matplotlib.pyplot as plt

I have faced the same error, I re-arranged the import order. It was working fine for me. Thanks

Thanks, it solved my problem as well. Any idea how this resolves the issue?

praveenydv · 2020-11-22T16:39:39Z

When I update pandas then problem got solved

TomAugspurger added the Needs Info Clarification about behavior needed to assess issue label Oct 8, 2018

WillAyd added the Can't Repro label Oct 8, 2018

TomAugspurger added the Visualization plotting label Oct 10, 2018

ghost mentioned this issue Dec 5, 2018

Unable to import pandas when using the gtk3 backend in ipython #19706

Closed

TomAugspurger closed this as completed Dec 6, 2018

gpoore mentioned this issue Mar 4, 2019

ValueError: module functions cannot set METH_CLASS or METH_STATIC gpoore/pythontex#144

Closed

jdtuck mentioned this issue Feb 19, 2020

undefined symbol: dorgqr_ jdtuck/fdasrsf_python#2

Closed

weihua916 mentioned this issue Nov 22, 2021

Value error snap-stanford/ogb#281

Closed

pyscripter mentioned this issue Nov 5, 2022

updated MethodCallback unit: now it don't work on FPC ARM64 pyscripter/python4delphi#387

Closed

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ValueError: module functions cannot set METH_CLASS or METH_STATIC #23040

ValueError: module functions cannot set METH_CLASS or METH_STATIC #23040

joh commented Oct 8, 2018

pambot commented Oct 8, 2018

TomAugspurger commented Oct 8, 2018 •

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joh commented Oct 10, 2018

TomAugspurger commented Oct 10, 2018

joh commented Oct 10, 2018

TomAugspurger commented Oct 10, 2018

Dominnio commented Oct 14, 2018

TomAugspurger commented Oct 14, 2018 via email

AlfTang commented Nov 8, 2018

lazka commented Dec 5, 2018

ghost commented Dec 5, 2018 •

edited by ghost

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TomAugspurger commented Dec 6, 2018

TheChymera commented Mar 4, 2019

lazka commented Mar 5, 2019

slaweksiluk commented Mar 7, 2019

dstreppa commented Nov 13, 2019 •

edited

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vigkrish92 commented Dec 17, 2019

masaduzz1 commented Jun 29, 2020

praveenydv commented Nov 22, 2020

ValueError: module functions cannot set METH_CLASS or METH_STATIC #23040

ValueError: module functions cannot set METH_CLASS or METH_STATIC #23040

Comments

joh commented Oct 8, 2018

Code Sample, a copy-pastable example if possible

Problem description

Expected Output

Output of pd.show_versions()

pambot commented Oct 8, 2018

TomAugspurger commented Oct 8, 2018 • edited Loading

joh commented Oct 10, 2018

TomAugspurger commented Oct 10, 2018

joh commented Oct 10, 2018

TomAugspurger commented Oct 10, 2018

Dominnio commented Oct 14, 2018

TomAugspurger commented Oct 14, 2018 via email

AlfTang commented Nov 8, 2018

lazka commented Dec 5, 2018

ghost commented Dec 5, 2018 • edited by ghost Loading

TomAugspurger commented Dec 6, 2018

TheChymera commented Mar 4, 2019

lazka commented Mar 5, 2019

slaweksiluk commented Mar 7, 2019

dstreppa commented Nov 13, 2019 • edited Loading

vigkrish92 commented Dec 17, 2019

masaduzz1 commented Jun 29, 2020

praveenydv commented Nov 22, 2020

Output of `pd.show_versions()`

TomAugspurger commented Oct 8, 2018 •

edited

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ghost commented Dec 5, 2018 •

edited by ghost

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dstreppa commented Nov 13, 2019 •

edited

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