python - pip error: unrecognized command line option ‘-fstack-protector-strong’

Question

When I sudo pip install pyquery, sudo pip install lxml, and sudo pip install cython, I get very similar output with the same error that says:

x86_64-linux-gnu-gcc: error: unrecognized command line option ‘-fstack-protector-strong’

Here's the complete pip output for sudo pip install pyquery:

Requirement already satisfied (use --upgrade to upgrade): pyquery in /usr/local/lib/python2.7/dist-packages
Downloading/unpacking lxml>=2.1 (from pyquery)
  Running setup.py egg_info for package lxml
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'
      warnings.warn(msg)
    Building lxml version 3.4.1.
    Building without Cython.
    Using build configuration of libxslt 1.1.28

Requirement already satisfied (use --upgrade to upgrade): cssselect in /usr/local/lib/python2.7/dist-packages/cssselect-0.9.1-py2.7.egg (from pyquery)
Installing collected packages: lxml
  Running setup.py install for lxml
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'
      warnings.warn(msg)
    Building lxml version 3.4.1.
    Building without Cython.
    Using build configuration of libxslt 1.1.28
    building 'lxml.etree' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/libxml2 -I/root/build/lxml/src/lxml/includes -I/usr/include/python2.7 -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o -w
    x86_64-linux-gnu-gcc: error: unrecognized command line option ‘-fstack-protector-strong’
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    Complete output from command /usr/bin/python -c "import setuptools;__file__='/root/build/lxml/setup.py';exec(compile(open(__file__).read().replace('
', '
'), __file__, 'exec'))" install --single-version-externally-managed --record /tmp/pip-gg4SuG-record/install-record.txt:
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'bugtrack_url'

  warnings.warn(msg)

Building lxml version 3.4.1.

Building without Cython.

Using build configuration of libxslt 1.1.28

running install

running build

running build_py

copying src/lxml/includes/lxml-version.h -> build/lib.linux-x86_64-2.7/lxml/includes

running build_ext

building 'lxml.etree' extension

x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/libxml2 -I/root/build/lxml/src/lxml/includes -I/usr/include/python2.7 -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o -w

x86_64-linux-gnu-gcc: error: unrecognized command line option ‘-fstack-protector-strong’

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

----------------------------------------
Command /usr/bin/python -c "import setuptools;__file__='/root/build/lxml/setup.py';exec(compile(open(__file__).read().replace('
', '
'), __file__, 'exec'))" install --single-version-externally-managed --record /tmp/pip-gg4SuG-record/install-record.txt failed with error code 1 in /root/build/lxml
Storing complete log in /root/.pip/pip.log

The complete log from /root/.pip/pip.log is here: http://pastebin.com/5R4VZDu8

I've looked at this, this, this, and this for help, but I haven't been able to solve the issue yet.

I've already installed libxml2-dev, libxslt1-dev, and python-dev. I'm running Debian 7.0 x64 on a DigitalOcean droplet.

I'm just trying to install pyquery. Can someone please help me out?

Thanks

Answer 1

I ran into this problem when I attempted to upgrade my pandas version to 0.15.2

If you install gcc-4.9 you are likely to still have an older version of gcc on your system (gcc-4.7 in my case).

I can think of 3 ways to solve this issue:

a) symlink /usr/bin/x86_64-linux-gnu-gcc to /usr/bin/x86_64-linux-gnu-gcc-4.9 if you want to be more organized about this use update-alternatives, see https://askubuntu.com/questions/26498/choose-gcc-and-g-version

b) figure out how to manually specify which compiler pip uses and set it in some sort of .conf file - I haven't examined where this file lives or if there are CLI options for pip that accomplish the equivalent. In principle, creating/editing a /usr/lib/pythonX.Y/distutils/distutils.cfg should do it. I ran into problems when I tried to use this approach.

c) Edit /usr/lib/python2.7/plat-x86_64-linux-gnu/_sysconfigdata_nd.py to reflect your updated compiler

How to use MinGW's gcc compiler when installing Python package using Pip? https://docs.python.org/2/install/#distutils-configuration-files

I went with the quick and dirty solution (a) to force everything to work

root@localhost:/home/user1$ rm /usr/bin/x86_64-linux-gnu-gcc
root@localhost:/home/user1$ ln -s /usr/bin/gcc-4.9 /usr/bin/x86_64-linux-gnu-gcc
root@localhost:/home/user1$ pip install pandas --upgrade
. . .  pandas compiles with gcc-4.9 here . . . 

move things back to how they were

root@localhost:/home/user1$ rm /usr/bin/x86_64-linux-gnu-gcc
root@localhost:/home/user1$ ln -s /usr/bin/gcc-4.7 /usr/bin/x86_64-linux-gnu-gcc