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('\r\n', '\n'), __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('\r\n', '\n'), __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
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
One possible solution would be to use GCC 4.9 or higher, which does support the -fstack-protector-strong flag.
Instead of upgrading to GCC 4.9, I was trying to find where the flag was defined and remove it. On Debian Wheezy, I found it in /usr/lib/python2.7/plat-x86_64-linux-gnu/_sysconfigdata_nd.py which belongs to the libpython2.7-minimal package. My solution was to replace all occurrences of -fstack-protector-strong with -fstack-protector within this file. Then pip install executed the correct build command.
Related
When am trying to install the memsql python library getting below error
I have tried the below options already:
sudo pip install memsql
sudo pip install memsql --global-option=build_ext --global-option="-I/usr/local/opt/openssl/include" --global-option="-L/usr/local/opt/openssl/lib"
Installing collected packages: MySQL-python, memsql
Running setup.py install for MySQL-python ... error
Complete output from command /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -u -c "import setuptools, tokenize;__file__='/private/tmp/pip-install-JDxMyP/MySQL-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" build_ext -I/usr/local/opt/openssl/include -L/usr/local/opt/openssl/lib install --record /private/tmp/pip-record-azfFw0/install-record.txt --single-version-externally-managed --compile:
running build_ext
building '_mysql' extension
creating build
creating build/temp.macosx-10.14-intel-2.7
cc -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -Dversion_info=(1,2,5,'final',1) -D__version__=1.2.5 -I/usr/local/Cellar/mysql/8.0.15/include/mysql -I/usr/local/opt/openssl/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c _mysql.c -o build/temp.macosx-10.14-intel-2.7/_mysql.o
_mysql.c:44:10: fatal error: 'my_config.h' file not found
#include "my_config.h"
^~~~~~~~~~~~~
1 error generated.
error: command 'cc' failed with exit status 1}
In order to install memsql-python you need to ensure that you have the dependencies already available. Specifically, the dependency that seems to be missing from your environment is libmysqlclient-dev or an equivalent package.
Note - you are overriding the include paths to point at your openssl installation which may be causing this issue due to how the compiler is searching for development headers.
According to the project's readme, use the following steps to get started quickly on Ubuntu:
sudo apt-get update
sudo apt-get install -y mysql-client python-dev libmysqlclient-dev python-pip
sudo pip install memsql
Use the following steps to get started with RHEL based distributions such as Amazon Linux or Centos:
sudo yum update
sudo yum install -y gcc mysql-devel
sudo pip install memsql
-- edit to address question regarding installation on Mac OSX
On a Mac it appears that you can install the mysql-client package from brew which in theory should provide the libmysqlclient-dev package. Once available try installing the memsql-python package without overriding linker flags since memsql-python should build fine without openssl. If you need openssl support then you will need to ensure that both the openssl and libmysqlclient-dev shared objects are available to the linker at compilation time.
This procedure worked for me:
brew remove mysql
brew install mysql#5.7
brew link --force mysql#5.7
I read a post and adjusted the procedure to link things in the /usr/local/bin instead of adding a new route to the PATH variable.
Reference: MacOS: "pip install MySQL-python" returning an error: "_mysql.c:44:10: fatal error: 'my_config.h' file not found"
I am trying to create a one to one real-time messaging system using Django. Upon searching I found out about django-channels. So i created a virtual env with python 3.5 and latest Django but when I do pip install channels I get :
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/kshitij/Documents/projects/personal/maker/venv/include/python3.5m -c src/twisted/test/raiser.c -o build/temp.linux-x86_64-3.5/src/twisted/test/raiser.o
#include "Python.h"
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
probably because of missing python headers so i did : sudo apt-get install python3-dev but it still shows the same error. What should I do?
pip version: 18
python version: 3.5
django version: 2.1
I tried doing sudo apt-get install python3-dev but getting:
ImportError: cannot import name '_BACKCOMPAT_MAGIC_NUMBER'
Verify your pip is not pip and its pip3.
You may also try installing sudo apt install python3.X-dev.
For you, it's sudo apt install python3.5-dev
Try installing the Linux compiler and python3-dev:
sudo apt install gcc
sudo apt install python3-dev
pip install channels
The last error may indicates you have an issue caused by many python versions installed on your system (see this answer). You should make sure you don't have incomplete or corrupted python installation on your system (did you already compiled Python by yourself?). In addition, make sure the package python3 is correctly installed or sudo apt-get install python3-dev cannot succeed.
In addition, you may try to locate Python.h on your system. Make sure each Python.h on your system correspond to a valid python setup (you may have one for python 2 and one more for python 3).
I understand some dependencies need to be satisfied before installing cartopy and basemap. I sorted out most of them using pip (like numpy etc.).
I found out there are some cartopy issues with Proj.4 and some basemap issues with GEOS.
I thought the python bindings to the Java project Proj.4 were enough and I am a bit lost with the C++ library GEOS (I think GDAL is enough for GEOS, I've linked it to the python world this way: pip install --global-option=build_ext --global-option="-I/usr/include/gdal" GDAL==`gdal-config --version).
I would prefer avoiding all those things like anaconda, canopy, etc.
If possible I would like to use only pip on both Ubuntu (apt-get, only if pip is not enough) and Mac OSX (homebrew e.g. brew install <some_package>, only if pip is not enough).
cartopy gets stuck on a version of Proj.4 that is too old. The pip output says: Proj4 version 4.8.0 is installed, but cartopy requires at least version 4.9.0..
I was assuming this pip install of the python bindings was enough, but it does not solve the problem:
$ pip show pyproj
Name: pyproj
Version: 1.9.5.1
Summary: Python interface to PROJ.4 library
Home-page: https://github.com/jswhit/pyproj
Author: Jeff Whitaker
Author-email: jeffrey.s.whitaker#noaa.gov
License: OSI Approved
Location: /usr/local/lib/python2.7/dist-packages
Requires:
I don't get why the python bindings to Proj.4 are not enough, even if those bindings are the latest version available using pip.
basemap is stuck in different ways:
Using pip2 install basemap somehow I get Could not find a version that satisfies the requirement basemap (from versions: )
No matching distribution found for basemap
But then from the basemap documentation I found that library is not linked to the pip repositories for some reason and needs to be installed from the source code. So I've run: pip2 install https://github.com/matplotlib/basemap/archive/v1.0.7rel.tar.gz and I believe that a GEOS compilation of the C++ code is triggered and after a while it stops with at the bottom this:
In file included from src/_geoslib.c:255:0:
/usr/include/geos_c.h:151:22: note: expected ‘GEOSMessageHandler’ but argument is of type ‘void (*)(char *, char *)’
extern void GEOS_DLL initGEOS(GEOSMessageHandler notice_function,
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/src/_geoslib.o -lgeos_c -lgeos -o build/lib.linux-x86_64-2.7/_geoslib.so
/usr/bin/ld: cannot find -lgeos
collect2: error: ld returned 1 exit status
/usr/bin/ld: cannot find -lgeos
collect2: error: ld returned 1 exit status
error: Command "x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/src/_geoslib.o -lgeos_c -lgeos -o build/lib.linux-x86_64-2.7/_geoslib.so" failed with exit status 1
----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-QVrKRr-build/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-EgAOPT-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-QVrKRr-build/
I am not sure what I am doing wrong:
how to provide the correct Proj.4 stuff to cartopy? Actually I would prefer finding an older version of cartopy that is fine with the existing version of Proj.4 (which I am assuming comes from the pip install bindings)
how to get basemap finding GEOS from the GDAL links I've setup with pip? If that's not enough, then what should I do more? Perhaps some apt-get of a GEOS pakcage that avoids triggering the GEOS compilation inside the basemap installation?
I am a bit confused in this no mans land between Java binaries, C++ binaries and bindings to python packages.
As you noticed cartopy requires Proj.4 lib in version >=4.9. On Ubuntu (newer than 16.04) you can install it through sudo apt-get install libproj-dev.
For older Ubuntu, e.g. 14.04, you could simply download newest package from 16.04 (xenial libproj-dev) and install it manually. Notice that it depends on libproj9 in version 4.9. Remember to remove older version before you update them with
sudo apt-get purge libproj-dev libproj9
Once you done that, open and download packages from links for appropriate architecture (from your log I understand that's amd64). Double click downloaded files in order librproj9 and libproj-dev or use
sudo dpkg -i <path_to_file>.
Please don't call this a duplicate.
All the answers have so far only 'solved' the problem by installing the ldap and other development packages globally, which doesn't solve the problem of not being able to install the python-ldap package in the virtual environment.
Examples include:
How do I install python-ldap in a virtualenv on Ubuntu?
sudo apt-get install libsasl2-dev python-dev libldap2-dev libssl-dev
I am using ubuntu 14.04, python 2.7 and flask in my virtual environment.
When I run pip install python-ldap, I receive the following error.
copying Lib/ldap/schema/__init__.py -> build/lib.linux-x86_64-2.7/ldap/schema
copying Lib/ldap/schema/models.py -> build/lib.linux-x86_64-2.7/ldap/schema
copying Lib/ldap/schema/subentry.py -> build/lib.linux-x86_64-2.7/ldap/schema
copying Lib/ldap/schema/tokenizer.py -> build/lib.linux-x86_64-2.7/ldap/schema
copying Lib/ldap/syncrepl.py -> build/lib.linux-x86_64-2.7/ldap
file Lib/ldap.py (for module ldap) not found
file Lib/ldap/controls.py (for module ldap.controls) not found
file Lib/ldap/extop.py (for module ldap.extop) not found
file Lib/ldap/schema.py (for module ldap.schema) not found
running egg_info
writing requirements to Lib/python_ldap.egg-info/requires.txt
writing Lib/python_ldap.egg-info/PKG-INFO
writing top-level names to Lib/python_ldap.egg-info/top_level.txt
writing dependency_links to Lib/python_ldap.egg-info/dependency_links.txt
warning: manifest_maker: standard file '-c' not found
file Lib/ldap.py (for module ldap) not found
file Lib/ldap/controls.py (for module ldap.controls) not found
file Lib/ldap/extop.py (for module ldap.extop) not found
file Lib/ldap/schema.py (for module ldap.schema) not found
reading manifest file 'Lib/python_ldap.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'Makefile'
warning: no files found matching 'Modules/LICENSE'
writing manifest file 'Lib/python_ldap.egg-info/SOURCES.txt'
running build_ext
building '_ldap' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/Modules
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DHAVE_SASL -DHAVE_TLS -DHAVE_LIBLDAP_R -DHAVE_LIBLDAP_R -DLDAPMODULE_VERSION=2.4.21 -IModules -I/usr/include -I/usr/include/sasl -I/usr/local/include -I/usr/local/include/sasl -I/usr/include/python2.7 -c Modules/LDAPObject.c -o build/temp.linux-x86_64-2.7/Modules/LDAPObject.o
Modules/LDAPObject.c:18:18: fatal error: sasl.h: No such file or directory
#include <sasl.h>
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Command "/home/kmertig/hd_request/hd_request/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-V4vhsl/python-ldap/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-NIR67Y-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/kmertig/hd_request/hd_request/include/site/python2.7/python-ldap" failed with error code 1 in /tmp/pip-build-V4vhsl/python-ldap
If I try to pip install any of the suggested dev libraries so that they are inside my virtual environment, I get the following error.
Could not find a version that satisfies the requirement libsasl2-dev (from versions: ) No matching distribution found for libsasl2-dev
I can install all this stuff globally just fine, but that just plain defeats the purpose of using virtualenv.
I would really like to find a meaningful, virtualenv solution, since all I have been able to find is non-virtualenv solutions for a virtualenv question.
Thanks.
The Python package python-ldap requires some other libs (libsasl2-dev, …) which are not python libs (so you can't use pip to install them). So, to use them, you have to install them. Two solutions:
use your package manager to install them (ex.: apt-get) ;
download their source code and compile them locally (in your virtualenv) (useful for some libs in special cases).
Maybe you can try the second solution?
having installed IPOPT and trying to install pyipopt in Ubuntu 12.04 box, I encountered the following error:
python setup.py install
results in the following error:
running install
running build
running build_py
running build_ext
building 'pyipoptcore' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/local/include/coin/ -I/usr/include/python2.7 -c src/callback.c -o build/temp.linux-x86_64-2.7/src/callback.o
In file included from src/callback.c:36:0:
src/hook.h:5:29: fatal error: IpStdCInterface.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1
any ideas ?
this is the interface for the ipopt library which is required to compile. as stated in the setup.py file
# You will probably have to edit this file in unpredictable ways
# if you want pyipopt to work for you, sorry.
the easiest way to handle this is to adjust the setup.py accordingly:
# When I installed Ipopt from source, I used the
# --prefix=/usr/local
# option, so this is where I want pyipopt to look for my ipopt installation.
# I only installed from source because the ipopt packaging
# for my linux distribution was buggy,
# so by the time you read this the bugs have probably been fixed
# and you will want to specify a different directory here.
IPOPT_DIR = '/usr/local/'
adjust IPOPT_DIR to the path where the library has been installed on your system, which of course should has been conducted anyway.
EDIT:
If you are installing from source, just use --prefix=/usr/local for the configure script and compile and install the library by running make; sudo make install. Then you don't have to change the setup.py file.