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I am having some issue with installing mysqlclient in a Docker conatiner hat was made by a mysql optimized Docker image (mysql/mysql-server). The container runs on an Oracle Linux Sysrem (CentOS).

The error looks like this 

Installing collected packages: mysqlclient, raven, redis, xmltodict, responses
  Running setup.py install for mysqlclient ... error
    Complete output from command /tracking_api/tracking/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-z_jafqw3/mysqlclient/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-vqelrf7r/install-record.txt --single-version-externally-managed --compile --install-headers /tracking_api/tracking/include/site/python3.6/mysqlclient:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    copying _mysql_exceptions.py -> build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/__init__.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/compat.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/connections.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/converters.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/cursors.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/release.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/times.py -> build/lib.linux-x86_64-3.6/MySQLdb
    creating build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/__init__.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/CLIENT.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/CR.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/ER.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/FIELD_TYPE.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/FLAG.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/REFRESH.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    running build_ext
    building '_mysql' extension
    creating build/temp.linux-x86_64-3.6
    gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Dversion_info=(1,3,12,'final',0) -D__version__=1.3.12 -I/usr/include/mysql -I/tracking_api/tracking/include -I/usr/include/python3.6m -c _mysql.c -o build/temp.linux-x86_64-3.6/_mysql.o -m64
    unable to execute 'gcc': No such file or directory
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/tracking_api/tracking/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-z_jafqw3/mysqlclient/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-vqelrf7r/install-record.txt --single-version-externally-managed --compile --install-headers /tracking_api/tracking/include/site/python3.6/mysqlclient" failed with error code 1 in /tmp/pip-install-z_jafqw3/mysqlclient/

I noticed that the issue was caused because there was no gcc in the container. After installing gcc with yum install gcc, I received another error that looks like this

Installing collected packages: mysqlclient, raven, redis, xmltodict, responses
  Running setup.py install for mysqlclient ... error
    Complete output from command /tracking_api/tracking/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-90ek02_q/mysqlclient/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-rdg1c3go/install-record.txt --single-version-externally-managed --compile --install-headers /tracking_api/tracking/include/site/python3.6/mysqlclient:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    copying _mysql_exceptions.py -> build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/__init__.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/compat.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/connections.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/converters.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/cursors.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/release.py -> build/lib.linux-x86_64-3.6/MySQLdb
    copying MySQLdb/times.py -> build/lib.linux-x86_64-3.6/MySQLdb
    creating build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/__init__.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/CLIENT.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/CR.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/ER.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/FIELD_TYPE.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/FLAG.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/REFRESH.py -> build/lib.linux-x86_64-3.6/MySQLdb/constants
    running build_ext
    building '_mysql' extension
    creating build/temp.linux-x86_64-3.6
    gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Dversion_info=(1,3,12,'final',0) -D__version__=1.3.12 -I/usr/include/mysql -I/tracking_api/tracking/include -I/usr/include/python3.6m -c _mysql.c -o build/temp.linux-x86_64-3.6/_mysql.o -m64
    _mysql.c:29:19: fatal error: mysql.h: No such file or directory
     #include "mysql.h"
                       ^
    compilation terminated.
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/tracking_api/tracking/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-90ek02_q/mysqlclient/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-rdg1c3go/install-record.txt --single-version-externally-managed --compile --install-headers /tracking_api/tracking/include/site/python3.6/mysqlclient" failed with error code 1 in /tmp/pip-install-90ek02_q/mysqlclient/

I realised that this was caused by the fact that mysql.h does not exist. I found in this question, that I can check weather the file exists. However, it seems that the mysql folder does not exists in the /use/local/ directory.

And this is what caused m confusion. Does anybody have any idea why did this happened? Why isn't there a mysql.h file when the docker image itself is mysql optimized? Thanks in advance.

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2 Answers 2

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1

You need to install mysql-community-devel, the mysql.h is in this package.

Note: you need first to uninstall mysql-community-server-minimal, and reinstall it after mysqlclient install done. Otherwise, you will encountered following conflict:

Transaction check error: file /usr/bin/mysql_config from install of mysql-community-devel-8.0.13-1.el7.x86_64 conflicts with file from package mysql-community-server-minimal-8.0.13-1.el7.x86_64

Steps as follows:(omit pip install)

yum remove -y mysql-community-server-minimal
yum install -y gcc
yum install -y mysql-community-devel
pip install mysqlclient
yum remove -y mysql-community-devel
yum install -y mysql-community-server-minimal

The output of mysqlclient install:

# pip install mysqlclient
Collecting mysqlclient
  Using cached https://files.pythonhosted.org/packages/ec/fd/83329b9d3e14f7344d1cb31f128e6dbba70c5975c9e57896815dbb1988ad/mysqlclient-1.3.13.tar.gz
Installing collected packages: mysqlclient
  Running setup.py install for mysqlclient ... done
Successfully installed mysqlclient-1.3.13
You are using pip version 8.1.2, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Finally, your last question:

Why isn't there a mysql.h file when the docker image itself is mysql optimized

From the dockerhub, you can find the link of mysql/mysqlserver dockerfile, it is in here:

FROM oraclelinux:7-slim

ARG MYSQL_SERVER_PACKAGE=mysql-community-server-minimal-8.0.13
ARG MYSQL_SHELL_PACKAGE=mysql-shell-8.0.13

# Install server
RUN yum install -y https://repo.mysql.com/mysql-community-minimal-release-el7.rpm \
      https://repo.mysql.com/mysql-community-release-el7.rpm \
  && yum-config-manager --enable mysql80-server-minimal \
  && yum install -y \
      $MYSQL_SERVER_PACKAGE \
      $MYSQL_SHELL_PACKAGE \
      libpwquality \
  && yum clean all \
  && mkdir /docker-entrypoint-initdb.d

VOLUME /var/lib/mysql

COPY docker-entrypoint.sh /entrypoint.sh
COPY healthcheck.sh /healthcheck.sh
ENTRYPOINT ["/entrypoint.sh"]
HEALTHCHECK CMD /healthcheck.sh
EXPOSE 3306 33060
CMD ["mysqld"]

From above, you can see it just use the pre-built mysql server package, did not compile the source code of mysql server, so it no needs for mysql.h, which is only used when do source build.

But when you install mysqlclient use pip, as mysqlclient python package has C extension dependency, so it will have to use gcc to build, then it needs mysql.h, this made you in trouble. After install mysql.h, everything is ok.

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0

You can simply do

    yum install -y --downloadonly --downloaddir=manual-install mysql-devel  && \
    rpm -i --force manual-install/*.rpm

this downloads the mysql-devel packages without installing, then installs using using directly the rpm commnad, that allows to force install

Wonder why yum nor microdnf have a --force param

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