pip install mysqlclient failed "Running setup.py bdist_wheel for mysqlclient ... error"

Question

I'm trying to run my Python 3 project on my newly formatted Mac OS High Sierra 10.13.4, by first running pipenv install to get the dependencies, but that fails.

Specifically, the part where it fails to install dependencies is the mysqlclient part.

This error message shows up:

_mysql.c:1894:3: error: use of undeclared identifier 'my_bool'
              my_bool recon = reconnect;
              ^
_mysql.c:1895:58: error: use of undeclared identifier 'recon'
              mysql_options(&self->connection, MYSQL_OPT_RECONNECT, &recon);
                                                                     ^

Configuration

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> python --version
Python 2.7.10

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> python3 --version
Python 3.6.5

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> brew install mysql-connector-c
Warning: mysql-connector-c 6.1.11 is already installed, its just not linked
You can use `brew link mysql-connector-c` to link this version.

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> brew link mysql-connector-c
Linking /usr/local/Cellar/mysql-connector-c/6.1.11... 
Error: Could not symlink bin/my_print_defaults
Target /usr/local/bin/my_print_defaults
is a symlink belonging to mysql. You can unlink it:
  brew unlink mysql

To force the link and overwrite all conflicting files:
  brew link --overwrite mysql-connector-c

To list all files that would be deleted:
  brew link --overwrite --dry-run mysql-connector-c

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> mysql --version
mysql  Ver 8.0.11 for macos10.13 on x86_64 (MySQL Community Server - GPL)

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> brew install mysql
Warning: mysql 5.7.22 is already installed and up-to-date
To reinstall 5.7.22, run `brew reinstall mysql`

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> brew info openssl
openssl: stable 1.0.2o (bottled) [keg-only]
SSL/TLS cryptography library
https://openssl.org/
/usr/local/Cellar/openssl/1.0.2o_1 (1,791 files, 12.3MB)
  Poured from bottle on 2018-04-20 at 13:06:42
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/openssl.rb
==> Dependencies
Build: makedepend ✘
==> Options
--without-test
    Skip build-time tests (not recommended)
==> Caveats
A CA file has been bootstrapped using certificates from the SystemRoots
keychain. To add additional certificates (e.g. the certificates added in
the System keychain), place .pem files in
  /usr/local/etc/openssl/certs

and run
  /usr/local/opt/openssl/bin/c_rehash

This formula is keg-only, which means it was not symlinked into /usr/local,
because Apple has deprecated use of OpenSSL in favor of its own TLS and crypto libraries.

If you need to have this software first in your PATH run:
  echo 'export PATH="/usr/local/opt/openssl/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set:
    LDFLAGS:  -L/usr/local/opt/openssl/lib
    CPPFLAGS: -I/usr/local/opt/openssl/include

Full terminal error log

darrenkarlsapalo@admins-MacBook-Pro ~/g/t/thesis-nltk> pip install mysqlclient
Collecting mysqlclient
  Using cached https://files.pythonhosted.org/packages/6f/86/bad31f1c1bb0cc99e88ca2adb7cb5c71f7a6540c1bb001480513de76a931/mysqlclient-1.3.12.tar.gz
Building wheels for collected packages: mysqlclient
  Running setup.py bdist_wheel for mysqlclient ... error
  Complete output from command /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/75/hg3nj2sx13567pbv76wdycqm0000gn/T/pip-install-mj5god72/mysqlclient/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /private/var/folders/75/hg3nj2sx13567pbv76wdycqm0000gn/T/pip-wheel-_frnx3t4 --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-x86_64-3.6
  copying _mysql_exceptions.py -> build/lib.macosx-10.9-x86_64-3.6
  creating build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  copying MySQLdb/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  copying MySQLdb/compat.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  copying MySQLdb/connections.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  copying MySQLdb/converters.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  copying MySQLdb/cursors.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  copying MySQLdb/release.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  copying MySQLdb/times.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
  creating build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  copying MySQLdb/constants/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  copying MySQLdb/constants/CLIENT.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  copying MySQLdb/constants/CR.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  copying MySQLdb/constants/ER.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  copying MySQLdb/constants/FIELD_TYPE.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  copying MySQLdb/constants/FLAG.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  copying MySQLdb/constants/REFRESH.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
  running build_ext
  building '_mysql' extension
  creating build/temp.macosx-10.9-x86_64-3.6
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch x86_64 -g -Dversion_info=(1,3,12,'final',0) -D__version__=1.3.12 -I/usr/local/mysql/include -I/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c _mysql.c -o build/temp.macosx-10.9-x86_64-3.6/_mysql.o
  _mysql.c:1894:3: error: use of undeclared identifier 'my_bool'
                  my_bool recon = reconnect;
                  ^
  _mysql.c:1895:58: error: use of undeclared identifier 'recon'
                  mysql_options(&self->connection, MYSQL_OPT_RECONNECT, &recon);
                                                                         ^
  2 errors generated.
  error: command 'gcc' failed with exit status 1

  ----------------------------------------
  Failed building wheel for mysqlclient
  Running setup.py clean for mysqlclient
Failed to build mysqlclient
Installing collected packages: mysqlclient
  Running setup.py install for mysqlclient ... error
    Complete output from command /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/75/hg3nj2sx13567pbv76wdycqm0000gn/T/pip-install-mj5god72/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 /private/var/folders/75/hg3nj2sx13567pbv76wdycqm0000gn/T/pip-record-vkhrazcr/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.6
    copying _mysql_exceptions.py -> build/lib.macosx-10.9-x86_64-3.6
    creating build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    copying MySQLdb/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    copying MySQLdb/compat.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    copying MySQLdb/connections.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    copying MySQLdb/converters.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    copying MySQLdb/cursors.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    copying MySQLdb/release.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    copying MySQLdb/times.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb
    creating build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/CLIENT.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/CR.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/ER.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/FIELD_TYPE.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/FLAG.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    copying MySQLdb/constants/REFRESH.py -> build/lib.macosx-10.9-x86_64-3.6/MySQLdb/constants
    running build_ext
    building '_mysql' extension
    creating build/temp.macosx-10.9-x86_64-3.6
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch x86_64 -g -Dversion_info=(1,3,12,'final',0) -D__version__=1.3.12 -I/usr/local/mysql/include -I/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c _mysql.c -o build/temp.macosx-10.9-x86_64-3.6/_mysql.o
    _mysql.c:1894:3: error: use of undeclared identifier 'my_bool'
                    my_bool recon = reconnect;
                    ^
    _mysql.c:1895:58: error: use of undeclared identifier 'recon'
                    mysql_options(&self->connection, MYSQL_OPT_RECONNECT, &recon);
                                                                           ^
    2 errors generated.
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/75/hg3nj2sx13567pbv76wdycqm0000gn/T/pip-install-mj5god72/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 /private/var/folders/75/hg3nj2sx13567pbv76wdycqm0000gn/T/pip-record-vkhrazcr/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/75/hg3nj2sx13567pbv76wdycqm0000gn/T/pip-install-mj5god72/mysqlclient/

I'm frustrated enough to want to uninstall all my python installations, but I'm just afraid I might screw something up with Mac that relies on the prebuilt outdated Python version.

How can I get my dependencies to be installed correctly?

Answer 1

mysqlclient is not compatible with MySQL 8.0.11 at the time of this writing. Using MySQL v5.7.x will fix this issue (at least on macOS).

Answer 2

If you are using macOS

then can use this command

$ LDFLAGS=-L/usr/local/opt/openssl/lib pip install mysqlclient