undefined symbol: mysql_real_escape_string_quote

[ostrokach]

I am getting an error:

ImportError: /opt/conda/envs/_test/lib/python3.5/site-packages/_mysql.cpython-35m-x86_64-linux-gnu.so: undefined symbol: mysql_real_escape_string_quote

When trying to build a conda package with mysqlclient master branch. I think this is caused by commit #109?

[methane]

Thanks for using bleeding edge code and reporting issue.

I assume you use MySQL >= 5.7.4 when building extension module, and MySQL < 5.7.4 when running.

Could you try this?

$ mysql_config

$ ldd /opt/conda/envs/_test/lib/python3.5/site-packages/_mysql.cpython-35m-x86_64-linux-gnu.so

[ostrokach]

Thank you for your quick response!

$ ldd /opt/conda/envs/_test/lib/python3.5/site-packages/_mysql.cpython-35m-x86_64-linux-gnu.so

linux-vdso.so.1 =>  (0x00007fffb23f6000)
libmysqlclient.so.18 => /opt/conda/envs/_test/lib/python3.5/site-packages/../../libmysqlclient.so.18 (0x00007f3f980d7000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f3f97eb3000)
libm.so.6 => /lib64/libm.so.6 (0x00007f3f97c2f000)
librt.so.1 => /lib64/librt.so.1 (0x00007f3f97a27000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f3f97822000)
libpython3.5m.so.1.0 => /opt/conda/envs/_test/lib/python3.5/site-packages/../../libpython3.5m.so.1.0 (0x00007f3f972ff000)
libc.so.6 => /lib64/libc.so.6 (0x00007f3f96f6b000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f3f96c64000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f3f96a4e000)
/lib64/ld-linux-x86-64.so.2 (0x000055a204b8f000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f3f9684b000

[ostrokach]

I get this error message when I try to compile mysqlclient using the conda-forge docker container: condaforge/linux-anvil:latest.

Conda recipe is as follows:

package:
  name: mysqlclient
  version: "1.3.8.dev"

source:
  git_url: https://github.com/PyMySQL/mysqlclient-python.git

build:
  number: 0
  skip: True # [osx]

requirements:
  build:
    - python
    - mysql-connector-c
  run:
    - python
    - mysql-connector-c

test:
  imports:
    - MySQLdb

about:
  home: https://github.com/PyMySQL/mysqlclient-python
  license: GNU General Public License (GPL)
  summary: 'Python interface to MySQL'

[methane]

What is mysql_config output?

About build error on conda-forge, have you read README?
https://github.com/PyMySQL/mysqlclient-python#prerequisites

If you have, please paste build error.

[ostrokach]

Post deleted

[methane]

Stop writing unrelated logs.
"Lost connection to MySQL server" can be happen in many reasons.
And I'm not free tech support of MySQL.

[methane]

libmysqlclient.so.18 => /opt/conda/envs/_test/lib/python3.5/site-packages/../../libmysqlclient.so.18 (0x00007f3f980d7000)

I don't know anything about conda, but I suppose it provides own libmysqlclient.
And you may build mysqlclient-python with system libmysqlclient. It can cause such a
link error.

[ostrokach]

I think they could be related...

Anyway, mysqlclient README says that the dependencies are: python-dev libmysqlclient-dev.
These are the packages that are included in the conda build requirements.

mysql-client-c is a conda package containing MySQL Connector C 6.1.6: https://dev.mysql.com/downloads/connector/c/ (Linux - Generic (glibc 2.5) (x86, 64-bit), Compressed TAR Archive).

The same build works for mysqlclient 1.3.7.

[methane]

I think they could be related...

"Lost connection ..." error must not related.

[methane]

Again, I don't use conda and I don't know anything about conda.
Conda user forum must be better place to ask "how to build".

[ostrokach]

I have build many packages with conda before. This isn't the issue.

I was the person who contibuted the mysqlclient 1.3.7 conda package to bioconda, which has close to 3000 downloads to date.

I was just wondering what changes in mysqlclient master branch make the build fail, because I was hoping that the master branch would fix my (possibly unrelated) problem...

Some changes were introduced that break the compatibility between mysqlclient and mysql-connector-c version 6.1.6.

[methane]

You didn't post mysql_config output
You didn't post build error log in docker

If you're expert, you must know about how mysql_config is important.

[ostrokach]

mysql_config 
Usage: /opt/conda/envs/_test/bin/mysql_config [OPTIONS]
Options:
        --cflags         [-I/opt/conda/envs/_test/include]
        --cxxflags       [-I/opt/conda/envs/_test/include]
        --include        [-I/opt/conda/envs/_test/include]
        --libs           [-L/opt/conda/envs/_test/lib -lmysqlclient -lpthread -lm -lrt -ldl]
        --libs_r         [-L/opt/conda/envs/_test/lib -lmysqlclient -lpthread -lm -lrt -ldl]
        --plugindir      [/usr/local/mysql/lib/plugin]
        --socket         [/tmp/mysql.sock]
        --port           [0]
        --version        [6.1.6]
        --variable=VAR   VAR is one of:
                pkgincludedir [/opt/conda/envs/_test/include]
                pkglibdir     [/opt/conda/envs/_test/lib]
                plugindir     [/usr/local/mysql/lib/plugin]

[methane]

OK, it may pointing right place.

What is output of python setup.py build? In my env (Ubuntu):

$ python3 setup.py build_ext -if
running build_ext
building '_mysql' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Dversion_info=(1,3,7,'final',1) -D__version__=1.3.7 -I/usr/include/mysql -I/home/inada-n/pyenv/versions/3.5.2/include/python3.5m -c _mysql.c -o build/temp.linux-x86_64-3.5/_mysql.o -fabi-version=2 -fno-omit-frame-pointer
In file included from /usr/include/mysql/mysql.h:64:0,
...
gcc -pthread -shared -L/home/inada-n/pyenv/versions/3.5.2/lib build/temp.linux-x86_64-3.5/_mysql.o -L/usr/lib/x86_64-linux-gnu -lmysqlclient -lpthread -lz -lm -lrt -ldl -o build/lib.linux-x86_64-3.5/_mysql.cpython-35m-x86_64-linux-gnu.so
copying build/lib.linux-x86_64-3.5/_mysql.cpython-35m-x86_64-linux-gnu.so -> 
~/work/mysqlclient-python (master)
$ ldd _mysql.so
    linux-vdso.so.1 =>  (0x00007ffd299da000)
    libmysqlclient.so.20 => /usr/lib/x86_64-linux-gnu/libmysqlclient.so.20 (0x00007f1daba77000)
...

[ostrokach]

$ python setup.py build
running build
running build_py
copying MySQLdb/release.py -> build/lib.linux-x86_64-3.5/MySQLdb
running build_ext