GCC error in python virtual environment in docker

Question

I have a docker file where i am creating a virtual environment in python 2.7.15 and installing all required python dependencies for my project.

Some of the dependencies require gcc to compile like pandas, lz4 .. are failing with below error,

 pandas/io/sas/sas.c:4:20: fatal error: Python.h: No such file or directory
     #include "Python.h"
                        ^
    compilation terminated.
    error: command 'gcc' failed with exit status 1

Even i tired installing python-devel , gcc also in the docker. But doesn't help.

RUN yum install -y python-pip python-devel gcc

Dockerfile:

FROM registry-access-redhat-com.repo.lab.pl.*-*.com/rhel7.5

# CONFIGURE YUM
RUN rm -f /etc/yum.repos.d/*
ADD resources/yum.repos.d/* /etc/yum.repos.d/
RUN echo "sslverify=false" >> /etc/yum.conf

# INSTALL REQUIRED SYSTEM PACKAGES 
RUN yum install -y python-pip python-devel gcc && yum clean all && rm -rf /var/cache/yum
RUN yum install -y wget && yum clean all && rm -rf /var/cache/yum && wget http://repo.lab.pl.alcatel-lucent.com/eden-yum-releases/installation-packages-rpm/python-2.7.15-2.x86_64.rpm

RUN yum install -y python-2.7.15-2.x86_64.rpm && yum clean all && rm -rf /var/cache/yum

#DOWNLAOD LATEST PIP
RUN wget -P /tmp/ https://files.pythonhosted.org/packages/c2/d7/90f34cb0d83a6c5631cf71dfe64cc1054598c843a92b400e55675cc2ac37/pip-18.1-py2.py3-none-any.whl

#INSTALL PIP ON PYTHON 2.7.15
RUN LD_LIBRARY_PATH=/usr/local/lib /usr/local/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install --find-links /tmp --upgrade --no-index /tmp/pip-18.1-py2.py3-none-any.whl

# CREATE foo GROUP AND USER
RUN groupadd foo
RUN useradd -d /home/foo -ms /bin/bash -g foo foo

# SETUP BASHRC for foo user
COPY file/.bashrc /home/foo
COPY file/.bash_profile /home/foo
RUN chown foo:foo /home/foo/.bash_profile
RUN chown foo:foo /home/foo/.bashrc

# SET WORKING DIRECTORY TO /home/foo
WORKDIR /home/foo

#CREATE VIRTUAL ENVIRONMENT
RUN wget -P /tmp/ https://files.pythonhosted.org/packages/e7/16/da8cb8046149d50940c6110310983abb359bbb8cbc3539e6bef95c29428a/setuptools-40.6.2-py2.py3-none-any.whl
RUN wget -P /tmp/ https://files.pythonhosted.org/packages/7c/17/9b7b6cddfd255388b58c61e25b091047f6814183e1d63741c8df8dcd65a2/virtualenv-16.1.0-py2.py3-none-any.whl
RUN LD_LIBRARY_PATH=/usr/local/lib /usr/local/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install --find-links /tmp --upgrade --no-index /tmp/virtualenv-16.1.0-py2.py3-none-any.whl
RUN LD_LIBRARY_PATH=/usr/local/lib /usr/local/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install --find-links /tmp --upgrade --no-index /tmp/setuptools-40.6.2-py2.py3-none-any.whl
RUN LD_LIBRARY_PATH=/usr/local/lib /usr/local/bin/virtualenv -p /usr/local/bin/python2.7 enet
RUN chown -R foo:foo /home/foo/enet
RUN export LD_LIBRARY_PATH=/usr/local/lib
RUN source /home/foo/enet/bin/activate
RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install --find-links /tmp --upgrade --no-index /tmp/pip-18.1-py2.py3-none-any.whl

RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install scipy
RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install openpyxl
RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install confluent-kafka

RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install cython

RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install pandas

RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install lz4

How can i resolve this issue.

Try installing specific devel package yum install python27-devel, just in case. — vivekyad4v
– vivekyad4v, Commented Dec 12, 2018 at 9:04
Why the need for a virtual environment in a Docker container? — SiHa
– SiHa, Commented Dec 12, 2018 at 11:25
I also recommend deleting the shell dotfiles; they've come up in several SO questions and will not work how you expect. (docker run ... myapp does not launch a shell at all.) — David Maze
– David Maze, Commented Dec 12, 2018 at 12:04

binarym · Accepted Answer · 2018-12-12 12:11:12Z

1

I guess you should:

Install the python development files (as suggest in comment).
Use a -I switch in gcc command line to point the correct path for python include files.

answered Dec 12, 2018 at 12:11

binarym

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4 Comments

sophros Over a year ago

And install the developer package with headers before that as vivekyad4v suggests above.

PGS Over a year ago

@binarym I tried pip to include header files. but still doesnt work

RUN LD_LIBRARY_PATH=/usr/local/lib /usr/local/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install --global-option=build_ext --global-option="-I/usr/include/python2.7" --global-option="-L/usr/local/lib" pandas

. How to use gcc. I am not aware of this. Python.h files are present under /usr/include/python2.7

PGS Over a year ago

when i change the LD_LIBRARY PATH to /usr/include/python2.7. pandas module installed successfully but not it my virtualenv path. RUN LD_LIBRARY_PATH=/usr/local/lib /home/foo/enet/bin/python2.7 /tmp/pip-18.1-py2.py3-none-any.whl/pip install pandas. It is installing /usr/lib64

binarym Over a year ago

I guess the problem is you specify -I/usr/include/python2.7 but your python installation looks under /usr/local... And note that LD_LIBRARY_PATH is to specify path for dynamic libraries, not include file ;-) You must set up both LD_LIBRARY_PATH and -I correctly.

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