BUG: ERROR building development env using Docker

[NumberPiOso]

Pandas version checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pandas.

• I have confirmed this bug exists on the main branch of pandas.

Reproducible Example

docker build --tag pandas-numberpioso-env .

ERROR: Command errored out with exit status 1: /opt/conda/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/pandas/setup.py'"'"'; __file__='"'"'/home/pandas/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.


<details>
  Running setup.py develop for pandas
    ERROR: Command errored out with exit status 1:
     command: /opt/conda/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/pandas/setup.py'"'"'; __file__='"'"'/home/pandas/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
         cwd: /home/pandas/
    Complete output (25 lines):
    running develop
    running egg_info
    writing pandas.egg-info/PKG-INFO
    writing dependency_links to pandas.egg-info/dependency_links.txt
    writing entry points to pandas.egg-info/entry_points.txt
    writing requirements to pandas.egg-info/requires.txt
    writing top-level names to pandas.egg-info/top_level.txt
    reading manifest file 'pandas.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    /tmp/pip-build-env-lkhctcw3/overlay/lib/python3.8/site-packages/setuptools/command/easy_install.py:157: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    /tmp/pip-build-env-lkhctcw3/overlay/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    no previously-included directories found matching 'doc/build'
    warning: no previously-included files matching '*~' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: no previously-included files matching '#*' found anywhere in distribution
    warning: no previously-included files matching '*.py[ocd]' found anywhere in distribution
    adding license file 'LICENSE'
    running build_ext
    building 'pandas._libs.algos' extension
    /opt/conda/compiler_compat/ld: cannot find /lib64/libpthread.so.0
    /opt/conda/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
    collect2: error: ld returned 1 exit status
    error: command '/opt/conda/bin/gcc' failed with exit code 1
    ----------------------------------------
</details>

Issue Description

Last command python -m pip install -e . at the Dockerfile fails:

pandas/Dockerfile

Lines 42 to 48 in 5c757e9

	SHELL ["/bin/bash", "-c"]
	RUN . /opt/conda/etc/profile.d/conda.sh \
	&& conda activate base \
	&& cd "$pandas_home" \
	&& export \
	&& python setup.py build_ext -j 4 \
	&& python -m pip install -e .

Running manually those lines at docker image is successful until we arrive at this one
python -m pip install -e .

Expected Behavior

I would expect that the image should be successfully built

> docker build --tag pandas-numberpioso-env
Successfully built a3c5533304a3
Successfully tagged pandas-numberpioso-env:latest

Installed Versions

INSTALLED VERSIONS ------------------ commit : 5c757e9 python : 3.8.12.final.0 python-bits : 64 OS : Linux OS-release : 5.13.0-28-generic Version : #31~20.04.1-Ubuntu SMP Wed Jan 19 14:08:10 UTC 2022 machine : x86_64 processor : x86_64 byteorder : little LC_ALL : None LANG : en_US.UTF-8 LOCALE : en_US.UTF-8

pandas : 1.5.0.dev0+277.g5c757e9c4c.dirty
numpy : 1.19.4
pytz : 2021.3
dateutil : 2.8.2
pip : 21.3.1
setuptools : 59.8.0
Cython : 0.29.26
pytest : 6.2.5
hypothesis : 6.36.0
sphinx : 4.4.0
blosc : None
feather : None
xlsxwriter : 3.0.2
lxml.etree : 4.7.1
html5lib : 1.1
pymysql : None
psycopg2 : None
jinja2 : 2.11.3
IPython : 8.0.1
pandas_datareader: None
bs4 : 4.10.0
bottleneck : 1.3.2
fastparquet : 0.7.2
fsspec : 2021.11.0
gcsfs : 2021.11.0
matplotlib : 3.5.1
numba : 0.55.0
numexpr : 2.8.0
odfpy : None
openpyxl : 3.0.9
pandas_gbq : None
pyarrow : 6.0.1
pyreadstat : 1.1.4
pyxlsb : None
s3fs : 2021.11.0
scipy : 1.7.3
sqlalchemy : 1.4.30
tables : 3.6.1
tabulate : 0.8.9
xarray : 0.18.2
xlrd : 2.0.1
xlwt : 1.3.0
zstandard : None

[rendner]

I recognized the same problem some days ago.

To create the docker image I added the following two lines:

    && ln -s "$CONDA_BUILD_SYSROOT"/lib64/* /lib64/ || true \
    && ln -s "$CONDA_BUILD_SYSROOT"/usr/lib64/* /usr/lib64/ || true \

between these two lines:

pandas/Dockerfile

Lines 47 to 48 in 5c757e9

	&& python setup.py build_ext -j 4 \
	&& python -m pip install -e .

This ugly workaround seems to "fix" the problem.

[rendner]

You have to change the last line to python -m pip install --no-build-isolation -e . to make it work. I will create a PR with the fix.