I tried to install graph-tool on Mac OSX 10.10 using homebrew. The brew build process works fine, but when I try to import graph-tool I get the error described in this question.
Another problem with homebrew is that I always builds graph-tool for python2.7 and it installs the packages in the Python 2.7 sit-packages folder. But I want to use it with Python 3.4. These are the reasons why I tried to build graph-tool from source.
The ./configure command automatically uses Python 2.7, too. So I passed it the desired Python version with ./configure PYTHON=python3.4
It then detects the correct version as well as the related paths but crash with the following error:
configure: error:
Could not link test program to Python. Maybe the
main Python library has been installed in some non-standard library
path. If so, pass it to configure, via the LDFLAGS environment
variable.
Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"
======================================================================
ERROR!
You probably have to install the development version of the
Python package for your distribution. The exact name of this package varies
among them.
======================================================================
The error occurs with and without PYTHON variable set.
From the output of ./configure I can see that everything works fine except for the last line, which says:
checking consistency of all components of python development
environment... no
Whats does the above line mean and how do I properly install graph-tool on my maschine?
The error message is explaining exactly what needs to be done. Since python was installed in a non-standard path, you need to pass the flag LDFLAGS="-L/usr/non-standard-path/python/lib" pointing to the directory where the python libraries are located. This is most likely "/usr/local/lib", if you are using homebrew.
I was getting this error when I was trying to install graph-tool using outdated an autoconf / automake / pkg-config combination (installed using yum in CentOS 5.10). Installing those packages from source fixed the problem... although I'm not sure how this related to my python installation....
It worked for me by passing the variable PYTHON_EXTRA_LDFLAGS="-Wl,-stack_size,1000000 -F/usr/local/Cellar/python3/3.6.3/Frameworks -framework CoreFoundation".
In your case, it would be the path to the homebrew installation of python3.4.
The way I found out is that in the config.log, the error message shows the following:
configure:19023: checking python extra libraries
configure:19030: result: -ldl -framework CoreFoundation
configure:19037: checking python extra linking flags
configure:19044: result: -Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python
configure:19051: checking consistency of all components of python development environment
configure:19079: gcc -o conftest -g -O2 -DNDEBUG -I/usr/local/Cellar/python3/3.6.3/Frameworks/Python.framework/Versions/3.6/include/python3.6m -F/usr/local/Cellar/python3/3.6.3/Frameworks/ -Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python conftest.c -L/usr/local/opt/python3/Frameworks/Python.framework/Versions/3.6/lib -lpython3.6m -ldl -framework CoreFoundation -ldl -framework CoreFoundation >&5
clang: error: no such file or directory: 'Python.framework/Versions/3.6/Python'
The error seems to be path 'Python.framework/Versions/3.6/Python', that in a homebrew installation does not exist. I search for the same path in the config.log and I found this line:
PYTHON_EXTRA_LDFLAGS="-Wl,-stack_size,1000000 -framework CoreFoundation Python.framework/Versions/3.6/Python"
So, the solution for me was to pass this variable with the right path.
Related
I want to debug ARM application on devices like Android machine, i prefer to use gdb(ARM version) than gdb with gdbserver to debug, because there is a dashboard , a visual interface for GDB in Python.
It must cooperation with gdb(ARM version) on devices,so i need to cross compiling a ARM version of gdb with python, the command used shows below:
./configure --host=arm-linux-gnueabi --target=arm-linux-gnueabi --with-python=/usr/bin
But finally a error message appeared:
configure:8096: checking whether to use python
configure:8098: result: /usr/bin/
configure:8316: checking for python2.7
configure:8334: arm-linux-gnueabi-gcc -o conftest -g -O2 -I/usr/include/python2.7 -I/usr/include/python2.7 conftest.c -ldl -ltermcap -lm -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions >&5
In file included from /usr/include/python2.7/Python.h:8:0,
from conftest.c:50:
/usr/include/python2.7/pyconfig.h:15:52: fatal error: arm-linux-gnueabi/python2.7/pyconfig.h: No such file or directory
compilation terminated.
Then I find the line 15 in /usr/include/python2.7/pyconfig.h, as below:
# elif defined(__ARM_EABI__) && !defined(__ARM_PCS_VFP)
#include <arm-linux-gnueabi/python2.7/pyconfig.h>
Here is the point, I only have x86_64-linux-gnu/python2.7/pyconfig.h in /usr/include, how can I get the arm-linux-gnueabi/python2.7/pyconfig.h? I already apt-get install python2.7-dev.
I ran into this problem when attempting to cross-compile a python wrapper module built with SWIG, but it looks to me like it will happen to anyone cross compiling python-linked C code on a Debian system.
Apparently the Debian python-dev packages are not set up with the header files to facilitate a cross compile, but it is possible to go get them manually. I'm not sure if this is a python bug or a Debian package bug, and I haven't researched if it applies to other distros.
pyconfig.h sets preprocessor defines to tell the python source code about platform-depended things like endianness and data type sizes, so the proper pyconfig.h is definitely needed to correctly compile python source. Fortunately, the pyconfig.h file should be the only file you need to grab separately, and it is available from the Debian python-dev package for your target platform.
you can download the package file for armeabi or any other architecture from https://packages.debian.org/jessie/libpython2.7-dev and extract the include directory yourself, or you can use the following commands to download the package and copy the proper files for armeabi to /usr/local/include
wget http://security.debian.org/debian-security/pool/updates/main/p/python2.7/libpython2.7-dev_2.7.9-2+deb8u2_armel.deb
dpkg -x libpython2.7-dev_2.7.9-2_armel.deb libpython2.7-dev_2.7.9-2_armel_extracted
sudo cp -r libpython2.7-dev_2.7.9-2_armel_extracted/usr/include/arm-linux-gnueabi/ /usr/local/include/
rm -r libpython2.7-dev_2.7.9-2_armel*
Note that on some cross compilers you will have to add -I /usr/local/include to the compiler options if it does not search this location by default, but to me this is better than modifying /usr/include and risking your changes being wiped out by the OS
I have just installed Python 3.4 on my Windows 7 64-bit machine, using Anaconda/Condas.
When I run the "hello world" cython example I get this error:
[py34] C:\Users\Jon\Documents\GitHub\CythonFunctions\cython_funcs>python setup.py build_ext --inplace
running build_ext
building 'cython_funcs.hello' extension
C:\Anaconda\envs\py34\MinGW\bin\gcc.exe -mdll -O -Wall -IC:\Anaconda\envs\py34\include -IC:\Anaconda\envs\py34\include -c hello.c -o build\temp.win-amd64-3.4\Release\hello.o
writing build\temp.win-amd64-3.4\Release\hello.def
C:\Anaconda\envs\py34\MinGW\bin\gcc.exe -shared -s build\temp.win-amd64-3.4\Release\hello.o build\temp.win-amd64-3.4\Release\hello.def -LC:\Anaconda\envs\py34\libs -LC:\Anaconda\envs\py34\PCbuild\amd6
4 -lpython34 -lmsvcr100 -o C:\Users\Jon\Documents\GitHub\CythonFunctions\cython_funcs\cython_funcs\hello.pyd
build\temp.win-amd64-3.4\Release\hello.o:hello.c:(.text+0x314): undefined reference to `__imp__PyThreadState_Current'
build\temp.win-amd64-3.4\Release\hello.o:hello.c:(.text+0x493): undefined reference to `__imp__Py_NoneStruct'
build\temp.win-amd64-3.4\Release\hello.o:hello.c:(.text+0x97b): undefined reference to `__imp_PyExc_ImportError'
collect2.exe: error: ld returned 1 exit status
error: command 'C:\\Anaconda\\envs\\py34\\MinGW\\bin\\gcc.exe' failed with exit status 1
From searching stackoverflow and google, this error occurs when the gcc and python versions are not both either 32 bit or 64 bit.
I have checked that my Python is 64 bit. The MinGW that I have, as can be seen from the path below, was part of my Python installation. How can I check if it is 64 bit or not? Or could this error be due to something else?
Update:
Strangely, the Ipython cythonmagic command here works fine:
http://docs.cython.org/src/quickstart/build.html?highlight=cythonmagic
One way would be to conda remove libpython (this will cause distutils to not use mingw), and install Visual Studio 2010, and use that to compile.
Your gcc line is missing a define: -DMS_WIN64. Anaconda (I presume) have modified the file cygwinccompiler.py in Lib/distutils of 2.7 envs, but this modification is not present in the distutils of the 3.4 env. I was getting different errors to yours, but this change fixed my setup.
I ran into a similar problem with Anaconda but it worked when I stopped trying to compile in the py34 directory. Instead put your helloworld.pyx file (make sure you change it to that extension .pyx as well) in the Anaconda3 folder along with the setup.py and when you compile make sure you are in the Anaconda3 folder as well so C:\Anaconda3 python setup.py build_ext --inplace. If memory serves this ran just fine.
This might work for linking problems (to be done in a temporary directory; copy instead of cp if not in a msys2 environment)
gendef c:/Windows/System32/python34.dll
dlltool -U -d python34.def -l libpython34.dll.a
cp libpython34.dll.a c:/Python34/libs
If gendef is unable to access python34.dll, it can be copied using windows explorer before gendef command.
gendef is available at least with mingw-w64 packages.
I want to install the pyvlfeat package. It requires Boost.Python.
When I run the command
python.exe setup.py build
I receive the following message:
C:\Users\alex\Anaconda\Scripts\gcc.bat -DMS_WIN64 -mdll -O -Wall -IC:\Users\A
lexkow\AppData\Roaming\Python\Python27\site-packages\numpy\core\include -Ivlfeat
/ -IC:\Users\alex\Anaconda\include -IC:\Users\alex\Anaconda\PC -c vlfeat/m
ser/vl_erfill.cpp -o build\temp.win-amd64-2.7\Release\vlfeat\mser\vl_erfill.o -m
sse2 -O2 -fPIC -w
In file included from vlfeat/mser/vl_erfill.cpp:7:0:
vlfeat/mser/../py_vlfeat.h:18:28: fatal error: boost/python.hpp: No such file or
directory
Which tells me Boost.Python is not installed correctly on my computer, or that I don't launch the python install command correctly.
The package INSTALL instructions are :
Building the Module on a Unix System --
The C++ wrappers require Boost.Python to be installed:
$ sudo apt-get install boost-python1.35-dev
pyvlfeat uses distutils, so to build the library:
$ python setup.py build
As I am on Windows I can't sudo apt-get, so I downloaded boost 1.57.0 and extracted it into
C:\Program Files\boost\boost_1_57_0
It did not change the result. And now I don't know what I should do:
When I read the documentation
The section 3: "No-Install Quick Start" explains how to build an extension module called extending and test it by running a Python script called test_extending.py. I don't think that is what I want to achieve and it seems outdated because it talks about the bjam build driver.
The section 4: "Installing Boost.Python on your system" looks more interresting, but it says the information is in the Getting Started Guide, and it is not.
How to install Boost.Python on Windows 7 in order to install a python package ? ?
I am looking at the setup.py file. It looks like you can set BOOST_PATH at the top. You should set that to the correct path to the Boost you downloaded, I think.
I am building YouCompleteMe plugin of vim, following this document. When I run make I get the following error.
Linking CXX shared library /home/sagar/.vim/bundle/YouCompleteMe/python/ycm_core.so
/usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
What is this error?
I have installed pyenv to manage python versions. Is it causing problem?
Make the linker point to the .so (shared object) file and not the .a (static lib) file.
You can do this specifying the flag when running cmake:
cmake -G "Unix Makefiles" -DPYTHON_LIBRARY=/usr/local/lib/libpython2.7.so . ~/.vim/bundle/YouCompleteme/cpp
Do mind that even though you're using pyenv, YouCompleteMe build may point to an undesired
python build as they are not correctly auto-detected right now.
If you're having this problem, you should probably also specify the Python header files correctly:
cmake -G "Unix Makefiles" -DPYTHON_LIBRARY=/usr/local/lib/libpython2.7.so -DPYTHON_INCLUDE_DIR=/usr/local/include/python . ~/.vim/bundle/YouCompleteme/cpp
PS=(I'm assuming your headers are in that path, do check before)
Since some paths were different on my system from the accepted answer (both the CMake and the python lib ones) I'm posting an alternate solution for the above problem:
Make sure to have a shared library version of libpython2.7.so
$ locate libpython
/usr/lib/x86_64-linux-gnu/libpython2.7.so.1
Either create a symlink to it from where CMake expects it to be
sudo ln -s "/usr/lib/x86_64-linux-gnu/libpython2.7.so.1" "/usr/lib/libpython2.7.so"
or alternatively, as written in YCM's build script code, you could add additional CMake options to ensure the .so library is properly found
export EXTRA_CMAKE_ARGS="-DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1"
I am running Enthought Python 2.7 as well as default Python 2.7, Xcode 4.5.1 in Mac OS 10.8.2. I am trying to develop a speech to text converter in Python. I use Enthought Python as it allows me to record in 16000Hz, 1 Channel using pyaudio, which is needed for pocketsphinx to work.
I am trying to setup pocketsphinx using brew install pocketsphinx.
I get the following errors
Even manual installation using make and using default python results in same errors
Using brew doctor, I get
How do I successfully install pocketsphinx?
Here is my config.log
Homebrew logs pocketsphinx, sphinxbase
According to the log you have outdated version of the libsndfile installed. You have a header sndfile.h, but not sndfile.pc pkg-config file:
configure:14532: checking for SNDFILE
configure:14540: $PKG_CONFIG --exists --print-errors "sndfile"
Package sndfile was not found in the pkg-config search path.
Perhaps you should add the directory containing `sndfile.pc'
to the PKG_CONFIG_PATH environment variable
No package 'sndfile' found
configure:14543: $? = 1
configure:14558: $PKG_CONFIG --exists --print-errors "sndfile"
Package sndfile was not found in the pkg-config search path.
Perhaps you should add the directory containing `sndfile.pc'
to the PKG_CONFIG_PATH environment variable
No package 'sndfile' found
configure:14561: $? = 1
No package 'sndfile' found
configure:14589: result: no
configure:14603: checking sndfile.h usability
configure:14603: gcc -std=gnu99 -c -g -O2 -Wall -
I/Library/Frameworks/Python.framework/Versions/7.3/include/python2.7 -
I/Library/Frameworks/Python.framework/Versions/7.3/include/python2.7 conftest.c >&5
configure:14603: $? = 0
configure:14603: result: yes
To solve this problem either remove the header to not confuse the configure or install newer sndfile with pkg-config support.
Actually that should be fixed in sphinxbase as well, a bug report would be welcome.