pandas: BUG: Python 3.9 Polyfit sanity test emitted a warning

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Code Sample, a copy-pastable example

import pandas as pd

Problem description

When importing pandas using python 3.9.0 I get the following error:

python(81328,0x10d755dc0) malloc: can't allocate region
:*** mach_vm_map(size=18446744071827312640, flags: 100) failed (error code=3)
python(81328,0x10d755dc0) malloc: *** set a breakpoint in malloc_error_break to debug
init_dgelsd failed init
Traceback (most recent call last):
  File "/Users/paul/python/test/t.py", line 2, in <module>
    import pandas as pd
  File "/Users/paul/python/test/venv/lib/python3.9/site-packages/pandas/__init__.py", line 11, in <module>
    __import__(dependency)
  File "/Users/paul/python/test/venv/lib/python3.9/site-packages/numpy/__init__.py", line 286, in <module>
    raise RuntimeError(msg)
RuntimeError: Polyfit sanity test emitted a warning, most likely due to using a buggy Accelerate backend. If you compiled yourself, see site.cfg.example for information. Otherwise report this to the vendor that provided NumPy.
RankWarning: Polyfit may be poorly conditioned

Expected Output

Pandas should import without an error.

Output of `pd.show_versions()`

I am unable to run pd.show_versions() because the program crashes as soon as pandas is imported. I am installing pandas 1.1.3 on a Mac.

About this issue

Original URL
State: closed
Created 4 years ago
Comments: 16 (5 by maintainers)

Most upvoted comments

This one worked for me:

$ pip cache remove numpy
$ brew install openblas # make sure OpenBLAS is installed
$ OPENBLAS="$(brew --prefix openblas)" pip install numpy # let numpy's setup.py know where OpenBLAS is installed

+15

matthiasdiener on Oct 28, 2020

None of those workarounds work for me even in a clean virtual environment (3.9) and an empty pip cache

pip install matplotlib

always fails with

RuntimeError: Polyfit sanity test emitted a warning, most likely due to using a buggy Accelerate backend. If you compiled yourself, see site.cfg.example for information. Otherwise report this to the vendor that provided NumPy.
    RankWarning: Polyfit may be poorly conditioned

orome on Oct 28, 2020

Polyfit sanity test emitted a warning, most likely due to using a buggy Accelerate backend. If you compiled yourself, see site.cfg.example for information. Otherwise report this to the vendor that provided NumPy.

1.先安装 OpenBLAS $ brew install openblas 2. 然后指定 OpenBLAS 作为 BLAS 提供方, 安装 Numpy 和 pandas $ OPENBLAS=“$(brew --prefix openblas)” pip3 install numpy pandas

First run pip uninstall numpy 完美！

WillGhost on Dec 9, 2020

numpy 1.19.3 has 3.9 wheels up on pypi now

jreback on Oct 29, 2020

Now that numpy has the wheel I am able to install with no issues.

sanders41 on Nov 1, 2020

@matthiasdiener Just

$ pip cache remove numpy
$ brew install openblas 
$ OPENBLAS="$(brew --prefix openblas)" pip install numpy

does indeed work; but subsequent

pip install matplotlib

results in pages and pages or errors ending in

ERROR: Failed building wheel for matplotlib

followed by an attempt to build matplotlib, which ends in more pages of errors and

ERROR: Command errored out with exit status 1: /Users/Rax/Documents/Projects/Coding/Python/venvs/dataviz/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/b6/3rk65h797p7407x7d36sqn9c0000gn/T/pip-install-e0fr6lw0/matplotlib/setup.py'"'"'; __file__='"'"'/private/var/folders/b6/3rk65h797p7407x7d36sqn9c0000gn/T/pip-install-e0fr6lw0/matplotlib/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/b6/3rk65h797p7407x7d36sqn9c0000gn/T/pip-record-p4qzyrcr/install-record.txt --single-version-externally-managed --compile --install-headers /Users/Rax/Documents/Projects/Coding/Python/venvs/dataviz/include/site/python3.9/matplotlib Check the logs for full command output.

What am I doing wrong?