fatal error: 'mysql.h' file not found #685

Almenon · 2024-01-29T21:51:57Z

Almenon
Jan 29, 2024

What OS and which version do you use?

macOS 14

How did you installed mysql client library?

brew install mysql-client

Output from `pkg-config --cflags --libs mysqlclient`

`-I/opt/homebrew/Cellar/mysql-client/8.3.0/include/mysql -L/opt/homebrew/Cellar/mysql-client/8.3.0/lib -lmysqlclient`

How did you tried to install mysqlclient?

pip install mysqlclient

Output of building mysqlclient

Collecting mysqlclient
  Using cached mysqlclient-2.2.1.tar.gz (89 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: mysqlclient
  Building wheel for mysqlclient (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for mysqlclient (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [44 lines of output]
      # Options for building extension module:
        extra_compile_args: ['-I/opt/homebrew/Cellar/mysql/8.3.0/include/mysql', '-std=c99']
        extra_link_args: ['-L/opt/homebrew/Cellar/mysql/8.3.0/lib', '-lmysqlclient']
        define_macros: [('version_info', (2, 2, 1, 'final', 0)), ('__version__', '2.2.1')]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-14.2-arm64-cpython-311
      creating build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/release.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/cursors.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/connections.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/__init__.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/times.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/converters.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/_exceptions.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      creating build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/FLAG.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/CLIENT.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/__init__.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/ER.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/CR.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/FIELD_TYPE.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      running egg_info
      writing src/mysqlclient.egg-info/PKG-INFO
      writing dependency_links to src/mysqlclient.egg-info/dependency_links.txt
      writing top-level names to src/mysqlclient.egg-info/top_level.txt
      reading manifest file 'src/mysqlclient.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      adding license file 'LICENSE'
      writing manifest file 'src/mysqlclient.egg-info/SOURCES.txt'
      copying src/MySQLdb/_mysql.c -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      running build_ext
      building 'MySQLdb._mysql' extension
      creating build/temp.macosx-14.2-arm64-cpython-311
      creating build/temp.macosx-14.2-arm64-cpython-311/src
      creating build/temp.macosx-14.2-arm64-cpython-311/src/MySQLdb
      clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/opt/homebrew/opt/openssl/include -I/opt/homebrew/include "-Dversion_info=(2, 2, 1, 'final', 0)" -D__version__=2.2.1 -I/Users/almenon/.pyenv/versions/3.11.5/include/python3.11 -c src/MySQLdb/_mysql.c -o build/temp.macosx-14.2-arm64-cpython-311/src/MySQLdb/_mysql.o -I/opt/homebrew/Cellar/mysql/8.3.0/include/mysql -std=c99
      src/MySQLdb/_mysql.c:29:10: fatal error: 'mysql.h' file not found
      #include "mysql.h"
               ^~~~~~~~~
      1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for mysqlclient
Failed to build mysqlclient
ERROR: Could not build wheels for mysqlclient, which is required to install pyproject.toml-based projects

Answered by methane

Jan 30, 2024

See #688.
You are using innovation (beta) version of MySQL. Use MySQL 8.0 instead.

View full answer

Almenon · 2024-01-29T21:52:34Z

Almenon
Jan 29, 2024
Author

An alternative would be installing mysql via brew, but I get an error that way too. Note that I am using a mac with ARM architecture

0 replies

Almenon · 2024-01-29T22:24:04Z

Almenon
Jan 29, 2024
Author

Looks like this was due to a cursed combination of environment variables in my previous terminal. I opened up a fresh terminal and now I'm getting a new error:

$ pip install mysqlclient
"Exception: Can not find valid pkg-config name"
$ export PKG_CONFIG_PATH="$(brew --prefix)/opt/mysql-client/lib/pkgconfig"
$ pip install mysqlclient

Collecting mysqlclient
  Using cached mysqlclient-2.2.1.tar.gz (89 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: mysqlclient
  Building wheel for mysqlclient (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for mysqlclient (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [59 lines of output]
      Trying pkg-config --exists mysqlclient
      # Options for building extension module:
        extra_compile_args: ['-I/opt/homebrew/Cellar/mysql-client/8.3.0/include/mysql', '-std=c99']
        extra_link_args: ['-L/opt/homebrew/Cellar/mysql-client/8.3.0/lib', '-lmysqlclient']
        define_macros: [('version_info', (2, 2, 1, 'final', 0)), ('__version__', '2.2.1')]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-14.2-arm64-cpython-311
      creating build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/release.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/cursors.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/connections.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/__init__.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/times.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/converters.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      copying src/MySQLdb/_exceptions.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      creating build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/FLAG.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/CLIENT.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/__init__.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/ER.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/CR.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      copying src/MySQLdb/constants/FIELD_TYPE.py -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb/constants
      running egg_info
      writing src/mysqlclient.egg-info/PKG-INFO
      writing dependency_links to src/mysqlclient.egg-info/dependency_links.txt
      writing top-level names to src/mysqlclient.egg-info/top_level.txt
      reading manifest file 'src/mysqlclient.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      adding license file 'LICENSE'
      writing manifest file 'src/mysqlclient.egg-info/SOURCES.txt'
      copying src/MySQLdb/_mysql.c -> build/lib.macosx-14.2-arm64-cpython-311/MySQLdb
      running build_ext
      building 'MySQLdb._mysql' extension
      creating build/temp.macosx-14.2-arm64-cpython-311
      creating build/temp.macosx-14.2-arm64-cpython-311/src
      creating build/temp.macosx-14.2-arm64-cpython-311/src/MySQLdb
      clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include "-Dversion_info=(2, 2, 1, 'final', 0)" -D__version__=2.2.1 -I/Users/almenon/.pyenv/versions/3.11.5/include/python3.11 -c src/MySQLdb/_mysql.c -o build/temp.macosx-14.2-arm64-cpython-311/src/MySQLdb/_mysql.o -I/opt/homebrew/Cellar/mysql-client/8.3.0/include/mysql -std=c99
      src/MySQLdb/_mysql.c:527:9: error: call to undeclared function 'mysql_ssl_set'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
              mysql_ssl_set(&(self->connection), key, cert, ca, capath, cipher);
              ^
      src/MySQLdb/_mysql.c:527:9: note: did you mean 'mysql_close'?
      /opt/homebrew/Cellar/mysql-client/8.3.0/include/mysql/mysql.h:797:14: note: 'mysql_close' declared here
      void STDCALL mysql_close(MYSQL *sock);
                   ^
      src/MySQLdb/_mysql.c:1795:9: error: call to undeclared function 'mysql_kill'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
          r = mysql_kill(&(self->connection), pid);
              ^
      src/MySQLdb/_mysql.c:1795:9: note: did you mean 'mysql_ping'?
      /opt/homebrew/Cellar/mysql-client/8.3.0/include/mysql/mysql.h:525:13: note: 'mysql_ping' declared here
      int STDCALL mysql_ping(MYSQL *mysql);
                  ^
      src/MySQLdb/_mysql.c:2011:9: error: call to undeclared function 'mysql_shutdown'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
          r = mysql_shutdown(&(self->connection), SHUTDOWN_DEFAULT);
              ^
      3 errors generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for mysqlclient
Failed to build mysqlclient
ERROR: Could not build wheels for mysqlclient, which is required to install pyproject.toml-based projects

2 replies

methane Jan 30, 2024
Maintainer

See #688.
You are using innovation (beta) version of MySQL. Use MySQL 8.0 instead.

Answer selected by Almenon

Almenon Jan 30, 2024
Author

Thanks for the info. I ended up removing the mysql dependency but I'll follow the linked issue so I know when the homebrew version works again. I might add it back in the future.

Almenon · 2024-01-29T22:46:54Z

Almenon
Jan 29, 2024
Author

More info:

I just ran brew update and brew upgrade recently
pkg-config v0.29.2
same issue with brew installing mysql instead of mysqlclient
installed python 3.11 via pyenv. Installed pyenv via brew.

$ brew info openssl
==> openssl@3: stable 3.2.0 (bottled)
Cryptography and SSL/TLS Toolkit
https://openssl.org/
/opt/homebrew/Cellar/openssl@3/3.2.0_1 (6,805 files, 31.9MB) *
  Poured from bottle using the formulae.brew.sh API on 2023-12-08 at 16:32:31
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/o/openssl@3.rb
License: Apache-2.0
==> Dependencies
Required: ca-certificates ✔

$ clang --version
Apple clang version 15.0.0 (clang-1500.1.0.2.5)
Target: arm64-apple-darwin23.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

https://www.redhat.com/en/blog/new-warnings-and-errors-clang-16
Kind of weird that there is an error because according to the above link I shouldn't see an error till I am on clang 16.

0 replies

mfrager · 2024-10-08T19:11:49Z

mfrager
Oct 8, 2024

I was able to fix the issue by adding the following lines to my ~/.zshrc file. (I'm using "mysql-client" from Homebrew.)

export MYSQLCLIENT_LDFLAGS="-L/opt/homebrew/opt/mysql-client/lib -lmysqlclient -rpath /usr/local/mysql/lib"
export MYSQLCLIENT_CFLAGS="-I/opt/homebrew/opt/mysql-client/include -I/opt/homebrew/opt/mysql-client/include/mysql"

1 reply

mutantsan Dec 10, 2024

don't forget to do source ~/.zshrc after

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fatal error: 'mysql.h' file not found #685

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Almenon Jan 29, 2024

What OS and which version do you use?

How did you installed mysql client library?

Output from pkg-config --cflags --libs mysqlclient

How did you tried to install mysqlclient?

Output of building mysqlclient

Replies: 4 comments · 3 replies

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Almenon Jan 29, 2024 Author

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Almenon Jan 29, 2024 Author

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methane Jan 30, 2024 Maintainer

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mfrager Oct 8, 2024

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mutantsan Dec 10, 2024

Almenon
Jan 29, 2024

Output from `pkg-config --cflags --libs mysqlclient`

Replies: 4 comments 3 replies

Almenon
Jan 29, 2024
Author

Almenon
Jan 29, 2024
Author

methane Jan 30, 2024
Maintainer

Almenon Jan 30, 2024
Author

Almenon
Jan 29, 2024
Author

mfrager
Oct 8, 2024