I tried to install onnx on my linux machine and encountered issue when I use python3 -m pip install onnxas
/tmp/pip-install-7ajubmjo/onnx_08cda1ef5f1d460ab7b455210cf3083e/onnx/defs/sequence/defs.cc: In function ‘bool onnx::BuildSequenceMapBodyFunc(const onnx::FunctionBodyBuildContext&, const onnx::OpSchema&, onnx::FunctionProto&)’: /tmp/pip-install-7ajubmjo/onnx_08cda1ef5f1d460ab7b455210cf3083e/onnx/defs/sequence/defs.cc:675:40: error: no match for ‘operator[]’ (operand types are ‘google::protobuf::RepeatedPtrField<onnx::ValueInfoProto>’ and ‘int’)
seq_at_node.add_output(g_inputs[inputIndex].name());
[ 95%] Building CXX object CMakeFiles/onnx.dir/onnx/version_converter/helper.cc.o
CMakeFiles/onnx.dir/build.make:830: recipe for target 'CMakeFiles/onnx.dir/onnx/defs/sequence/defs.cc.o' failed
The protobuf was installed via sudo apt-get install protobuf-compiler libprotobuf-dev and my environment is:
- python=3.6
- ubuntu=18.04
Another related issue seems that the compilation cannot not find pybind11 as:
Generated: /tmp/pip-install-7ajubmjo/onnx_08cda1ef5f1d460ab7b455210cf3083e/.setuptools-cmake-build/onnx/onnx-ml.proto
Generated: /tmp/pip-install-7ajubmjo/onnx_08cda1ef5f1d460ab7b455210cf3083e/.setuptools-cmake-build/onnx/onnx-operators-ml.proto
Generated: /tmp/pip-install-7ajubmjo/onnx_08cda1ef5f1d460ab7b455210cf3083e/.setuptools-cmake-build/onnx/onnx-data.proto
-- Could NOT find pybind11 (missing: pybind11_DIR)
-- pybind11 v2.9.1
--
-- ******** Summary ********
-- CMake version : 3.10.2
-- CMake command : /usr/bin/cmake
-- System : Linux
-- C++ compiler : /usr/bin/c++
-- C++ compiler version : 7.5.0
-- CXX flags : -Wnon-virtual-dtor
even though it's already installed via pip install pybind11.
Any thoughts on how to move forward with this issue ?
Upgrade you protobuf version seems the issue is with default Ubuntu 18.04 repo protobuf package.
simmilar issue was reported on opencv forum.
github issue
Installation of protobuf 3.5.1 fixes this, maybe error in the original
install process. I installed protobuf 3.5.1 from this release
Install steps
./autogen.sh
./configure
make
make install
I am trying to install a Python package and I get this error in CentOS7:
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ModuleNotFoundError: No module named 'encodings'
Complete log is here: https://pastebin.com/raw/xs6zFKVg
Here is the package named Kaolin from NVIDIA: https://github.com/NVIDIAGameWorks/kaolin
This error happens after I switch to gcc 6.3 and enter this command: python setup.py install
How should I fix it?
Note that, initially I had GCC 7 and I used the following commands to move onto GCC 6.3 (seems like CUDA had compatability problem with GCC 7 so I had to switch):
$ sudo yum install devtoolset-6
and
$ scl enable devtoolset-6 bash
Now I have:
$ gcc --version
gcc (GCC) 6.3.1 20170216 (Red Hat 6.3.1-3)
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
I am not sure if what I did above was the best bet or if this must have caused this new issue.
I fixed the problem using the following commands:
$ conda create -p /scratch3/3d_pose/kaolin_env python=3.6 numpy cython pytorch-gpu "matplotlib<3.0.0" scikit-image shapely "trimesh>=3.0" scipy sphinx "pytest>=4.6" "pytest-cov>=2.7" tqdm Cython autopep8 flake8
$ conda activate /scratch3/3d_pose/kaolin_env
$ pip install pptk
$ python setup.py install
Still the import kaolin throws an error even from the .. of kaolin repo.
I seem to be one of the many people struggling to install gensim on windows. I have trawled through countless forums but the errors poster there never appear to match my errors. So hopefully someone can point me in the right direction!
I am running Windows Server 2012 R2 Standard 64-bit. I have installed MinGW & Anaconda 2.2.0 (64-bit), which comes with Python 2.7.9.
I have added a file distutils.cfg into C:\Users\Sam\Anaconda\Lib\distutils with the contents:
[build]
compiler=mingw32
I have added C:\MinGW\bin to my Environment variables.
If I install gensim using pip I do not get any errors, until I try to run Word2Vec when I get the error:
C:\Users\sam.passmore\AppData\Local\Continuum\Anaconda\lib\site-packages\gensim\models\word2vec.py:459: UserWarning: C extension com
pilation failed, training will be slow. Install a C compiler and reinstall gensim for fast training.
So I have uninstalled gensim and tried to re-install using the mingw32 compiler, but this gives me this error:
python setup.py build --compiler=mingw32
c:\users\sam.passmore\appdata\local\continuum\anaconda\lib\site-packages\setuptools-14.3-py2.7.egg\setuptools\dist.py:282: UserWarni
ng: Normalizing '0.11.1-1' to '0.11.1.post1'
running build
running build_ext
building 'gensim.models.word2vec_inner' extension
C:\MinGW\bin\gcc.exe -DMS_WIN64 -mdll -O -Wall -Igensim\models -IC:\Users\sam.passmore\AppData\Local\Continuum\Anaconda\include -IC:
\Users\sam.passmore\AppData\Local\Continuum\Anaconda\PC -IC:\Users\sam.passmore\AppData\Local\Continuum\Anaconda\lib\site-packages\n
umpy\core\include -c ./gensim/models/word2vec_inner.c -o build\temp.win-amd64-2.7\Release\.\gensim\models\word2vec_inner.o
gcc: error: ./gensim/models/word2vec_inner.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
command 'C:\\MinGW\\bin\\gcc.exe' failed with exit status 1
setup.py:82: UserWarning:
********************************************************************
WARNING: %s could not
be compiled. No C extensions are essential for gensim to run,
although they do result in significant speed improvements for some modules.
%s
Here are some hints for popular operating systems:
If you are seeing this message on Linux you probably need to
install GCC and/or the Python development package for your
version of Python.
Debian and Ubuntu users should issue the following command:
$ sudo apt-get install build-essential python-dev
RedHat, CentOS, and Fedora users should issue the following command:
$ sudo yum install gcc python-devel
If you are seeing this message on OSX please read the documentation
here:
http://api.mongodb.org/python/current/installation.html#osx
********************************************************************
The gensim.models.word2vec_inner extension moduleThe output above this warning shows how the compilation failed.
"The output above this warning shows how the compilation failed.")
building 'gensim.models.doc2vec_inner' extension
C:\MinGW\bin\gcc.exe -DMS_WIN64 -mdll -O -Wall -Igensim\models -IC:\Users\sam.passmore\AppData\Local\Continuum\Anaconda\include -IC:
\Users\sam.passmore\AppData\Local\Continuum\Anaconda\PC -IC:\Users\sam.passmore\AppData\Local\Continuum\Anaconda\lib\site-packages\n
umpy\core\include -c ./gensim/models/doc2vec_inner.c -o build\temp.win-amd64-2.7\Release\.\gensim\models\doc2vec_inner.o
gcc: error: ./gensim/models/doc2vec_inner.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
command 'C:\\MinGW\\bin\\gcc.exe' failed with exit status 1
setup.py:82: UserWarning:
********************************************************************
WARNING: %s could not
be compiled. No C extensions are essential for gensim to run,
although they do result in significant speed improvements for some modules.
%s
Here are some hints for popular operating systems:
If you are seeing this message on Linux you probably need to
install GCC and/or the Python development package for your
version of Python.
Debian and Ubuntu users should issue the following command:
$ sudo apt-get install build-essential python-dev
RedHat, CentOS, and Fedora users should issue the following command:
$ sudo yum install gcc python-devel
If you are seeing this message on OSX please read the documentation
here:
http://api.mongodb.org/python/current/installation.html#osx
********************************************************************
The gensim.models.doc2vec_inner extension moduleThe output above this warning shows how the compilation failed.
"The output above this warning shows how the compilation failed."
I have exhausted all options I can think of or find, so if anyone could give some advice it would be much appreciated.
I managed to solve this after using conda install for gensim, rather than pip.
conda install gensim
I am not sure what other steps I have included above have contributed to the answer, but this was the last thing I did before I no longer was getting the 'Install a C compiler and reinstall gensim for fast training.' message.
During my research in trying to solve this problem I saw that the most common methods were adding the lines
[build]
compiler=mingw32
to the distutils.cfg file as well as ensuring MinGW is in your path. Also ensuring that the MinGW bit version is the same as your python version.
Getting this error:
sudo: unable to resolve host coderw#ll
-- Could NOT find PythonLibs (missing: PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS)
CMake Error at /usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
(message):
Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE)
Call Stack (most recent call first):
/usr/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
(_FPHSA_FAILURE_MESSAGE)
/usr/share/cmake-2.8/Modules/FindPythonInterp.cmake:139
(FIND_PACKAGE_HANDLE_STANDARD_ARGS)
Code/cmake/Modules/FindNumPy.cmake:10 (find_package)
CMakeLists.txt:114 (find_package)
-- Configuring incomplete, errors occurred!
See also "/home/coderwall/Desktop/rdkit/build/CMakeFiles/CMakeOutput.log".
See also "/home/coderwall/Desktop/rdkit/build/CMakeFiles/CMakeError.log".
I have already installed:
sudo apt-get install python-dev
Environment variable are already set as follow:
PYTHON_INCLUDE_DIRS=/usr/include/python2.7
PYTHON_LIBRARIES=/usr/lib/python2.7/config/libpython2.7.so
Location of python.h : /usr/lib/include/python2.7/python.h
Location of python libs: /usr/lib/python2.7/
How to solve this?
You can fix the errors by appending to the cmake command the -DPYTHON_LIBRARY and -DPYTHON_INCLUDE_DIR flags filled with the respective folders.
Thus, the trick is to fill those parameters with the returned information from the python interpreter, which is the most reliable. This may work independently of your python location/version (also for Anaconda users):
$ cmake .. \
-DPYTHON_INCLUDE_DIR=$(python -c "import sysconfig; print(sysconfig.get_path('include'))") \
-DPYTHON_LIBRARY=$(python -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
If the version of python that you want to link against cmake is Python3.X and the default python symlink points to Python2.X, python3 -c ... can be used instead of python -c ....
In case that the error persists, you may need to update the cmake to a higher version as stated by #pdpcosta and repeat the process again.
For me this is helpful:
# if using python2
apt-get install python-dev
# if using python3
apt-get install python3-dev
I hit the same issue,and discovered the error message gives misleading variable names. Try setting the following (singular instead of plural):
PYTHON_INCLUDE_DIR=/usr/include/python2.7
PYTHON_LIBRARY=/usr/lib/python2.7/config/libpython2.7.so
The (plural) variables you see error messages about are values that the PythonLibs sets up when it is initialised correctly.
Even after adding -DPYTHON_INCLUDE_DIR and -DPYTHON_LIBRARY as suggested above, I was still facing the error Could NOT find PythonInterp. What solved it was adding -DPYTHON_EXECUTABLE:FILEPATH= to cmake as suggested in https://github.com/pybind/pybind11/issues/99#issuecomment-182071479:
cmake .. \
-DPYTHON_INCLUDE_DIR=$(python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())") \
-DPYTHON_LIBRARY=$(python -c "import distutils.sysconfig as sysconfig; print(sysconfig.get_config_var('LIBDIR'))") \
-DPYTHON_EXECUTABLE:FILEPATH=`which python`
I was facing this problem while trying to compile OpenCV 3 on a Xubuntu 14.04 Thrusty Tahr system.
With all the dev packages of Python installed, the configuration process was always returning the message:
Could NOT found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.6", minimum required is "2.7")
Could NOT find PythonLibs (missing: PYTHON_INCLUDE_DIRS) (found suitable exact version "2.7.6")
Found PythonInterp: /usr/bin/python3.4 (found suitable version "3.4", minimum required is "3.4")
Could NOT find PythonLibs (missing: PYTHON_LIBRARIES) (Required is exact version "3.4.0")
The CMake version available on Thrusty Tahr repositories is 2.8.
Some posts inspired me to upgrade CMake.
I've added a PPA CMake repository which installs CMake version 3.2.
After the upgrade everything ran smoothly and the compilation was successful.
Some last version of Ubuntu installs Python 3.4 by default and the CMake version from Ubuntu (2.8) only searches up to Python 3.3.
Try to add set(Python_ADDITIONAL_VERSIONS 3.4) before the find_package statement.
Remember to clean CMakeCache.txt too.
This problem can also happen in Windows. Cmake looks into the registry and sometimes python values are not set. For those with similar problem:
http://ericsilva.org/2012/10/11/restoring-your-python-registry-in-windows/
Just create a .reg file to set the necessary keys and edit accordingly to match your setup.
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Python]
[HKEY_CURRENT_USER\Software\Python\Pythoncore]
[HKEY_CURRENT_USER\Software\Python\Pythoncore\2.6]
[HKEY_CURRENT_USER\Software\Python\Pythoncore\2.6\InstallPath]
#="C:\\python26"
[HKEY_CURRENT_USER\Software\Python\Pythoncore\2.6\PythonPath]
#="C:\\python26;C:\\python26\\Lib\\;C:\\python26\\DLLs\\"
[HKEY_CURRENT_USER\Software\Python\Pythoncore\2.7]
[HKEY_CURRENT_USER\Software\Python\Pythoncore\2.7\InstallPath]
#="C:\\python27"
[HKEY_CURRENT_USER\Software\Python\Pythoncore\2.7\PythonPath]
#="C:\\python27;C:\\python27\\Lib\\;C:\\python27\\DLLs\\"
Note that if you are using cMake version 3.12 or later, variable PythonInterp and PythonLibs has been changed into Python.
So we use:
find_package(Python ${PY_VERSION} REQUIRED)
instead of:
find_package(PythonInterp ${PY_VERSION} REQUIRED)
find_package(PythonLibs ${PY_VERSION} REQUIRED)
see https://cmake.org/cmake/help/v3.12/module/FindPython.html for details.
I had upgraded to python3.8 on my system and had an incomplete install. Managed to fix it by installing the rest of the 3.8 packages:
sudo apt-get install python3.8 python3.8-dev python3.8-distutils python3.8-venv
Paste this into your CMakeLists.txt:
# find python
execute_process(COMMAND python-config --prefix OUTPUT_VARIABLE PYTHON_SEARCH_PATH)
string(REGEX REPLACE "\n$" "" PYTHON_SEARCH_PATH "${PYTHON_SEARCH_PATH}")
file(GLOB_RECURSE PYTHON_DY_LIBS ${PYTHON_SEARCH_PATH}/lib/libpython*.dylib ${PYTHON_SEARCH_PATH}/lib/libpython*.so)
if (PYTHON_DY_LIBS)
list(GET PYTHON_DY_LIBS 0 PYTHON_LIBRARY)
message("-- Find shared libpython: ${PYTHON_LIBRARY}")
else()
message(WARNING "Cannot find shared libpython, try find_package")
endif()
find_package(PythonInterp)
find_package(PythonLibs ${PYTHON_VERSION_STRING} EXACT)
In case that might help, I found a workaround for a similar problem, looking at the cmake doc :
https://cmake.org/cmake/help/v3.0/module/FindPythonLibs.html
You must set two env vars for cmake to find coherent versions.
Unfortunately this is not a generic solution...
cmake -DPYTHON_LIBRARY=${HOME}/.pyenv/versions/3.8.0/lib/libpython3.8.a -DPYTHON_INCLUDE_DIR=${HOME}/.pyenv/versions/3.8.0/include/python3.8/ cern_root/
In Python 3.2 and onward distutils.sysconfig is deprecated in favor of sysconfig.
To get all the variable names in data structure and inspect the situation we can use get_paths function
import sysconfig
sysconfig.get_paths()
which will return us a dict with all the relevant variable names as keys, and corresponding paths as values.
When we know the key we can get the value dynamically,
>>> sysconfig.get_path("include")
'C:\\Program Files\\Python310\\Include'
However, the most convenient feature of sysutils for this situation is that it can list all the variables at once from the command-prompt by invoking python -m sysconfig:
$ python -m sysconfig
Platform: "macosx-10.4-i386"
Python version: "3.2"
Current installation scheme: "posix_prefix"
Paths:
data = "/usr/local"
include = "/Users/tarek/Dev/svn.python.org/py3k/Include"
platinclude = "."
platlib = "/usr/local/lib/python3.2/site-packages"
platstdlib = "/usr/local/lib/python3.2"
purelib = "/usr/local/lib/python3.2/site-packages"
scripts = "/usr/local/bin"
stdlib = "/usr/local/lib/python3.2"
Variables:
AC_APPLE_UNIVERSAL_BUILD = "0"
AIX_GENUINE_CPLUSPLUS = "0"
AR = "ar"
ARFLAGS = "rc"
...
Maybe below command line works for you if all of above methods didn't work.
sudo apt-get install cython cython3
On Ubuntu 20 at least, since Python 2.7 is deprecated, you can:
sudo apt install python2.7-dev
And then PYTHON_INCLUDE_DIR can be set to /usr/include/python2.7
I can't seem to be able to get the python ldap module installed on my OS X Mavericks 10.9.1 machine.
Kernel details:
uname -a
Darwin 13.0.0 Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64 x86_64
I tried what was suggested here:
http://projects.skurfer.com/posts/2011/python_ldap_lion/
But when I try to use pip I get a different error
Modules/LDAPObject.c:18:10: fatal error: 'sasl.h' file not found
*#include sasl.h
I also tried what was suggested here:
python-ldap OS X 10.6 and Python 2.6
But with the same error.
I am hoping someone could help me out here.
using pieces from both #hharnisc and #mick-t answers.
pip install python-ldap \
--global-option=build_ext \
--global-option="-I$(xcrun --show-sdk-path)/usr/include/sasl"
A workaround
/usr/include appears to have moved
$ xcrun --show-sdk-path
$ sudo ln -s <the_path_from_above_command>/usr/include /usr/include
Now run pip install!
In my particular case, I couldn't simply use the pip arguments noted in other answers because I'm using it with tox to install dependencies from a requirements.txt file, and I need my tox.ini to remain compatible with non-Mac environments.
I was able to resolve this in much simpler fashion: exporting CFLAGS such that it adds an include path to the sasl headers already installed by Xcode:
$ pip install python-ldap
...
building '_ldap' extension
creating build/temp.macosx-10.10-x86_64-2.7
creating build/temp.macosx-10.10-x86_64-2.7/Modules
clang -fno-strict-aliasing -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_SASL -DHAVE_TLS -DHAVE_LIBLDAP_R -DHAVE_LIBLDAP_R -DLDAPMODULE_VERSION=2.4.19 -IModules -I/opt/openldap-RE24/include -I/usr/include/sasl -I/usr/include -I/Users/bc/.pyenv/versions/2.7.10/include/python2.7 -c Modules/LDAPObject.c -o build/temp.macosx-10.10-x86_64-2.7/Modules/LDAPObject.o
Modules/LDAPObject.c:18:10: fatal error: 'sasl.h' file not found
#include <sasl.h>
^
1 error generated.
error: command 'clang' failed with exit status 1
$ export CFLAGS="-I$(xcrun --show-sdk-path)/usr/include/sasl"
$ pip install python-ldap
...
Successfully installed python-ldap-2.4.19
Depending on whether or not you use any userspace-friendly Python tools (I use pyenv), you may have to prefix your pip commands with sudo.
I had the same problem. I'm using Macports on my Mac and I have cyrus-sasl2 installed which provides sasl.h in /opt/local/include/sasl/. You can pass options to build_ext using pip's global-option argument. To pass the include PATH to /opt/local/include/sasl/sasl.h run pip like this:
pip install python-ldap --global-option=build_ext --global-option="-I/opt/local/include/sasl"
Alternatively you could point it to whatever the output from xcrun --show-sdk-path provides. On my box that's:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
Then you need to determine the PATH to the sasl header files. For me that's:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/sasl/
Let me know if that helps or you need a hand.
I used a combination of posts I found about this problem (including this one) to eventually come up with this (copied from a larger script):
export XC_SDK=$(xcrun --show-sdk-path)
export USR_INC=$XC_SDK/usr/include
export PATH=$USR_INC:$PATH
echo "installing python-ldap"
ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future pip install python-ldap
You can test it with python -c "import ldap"
The main reason I didn't follow the advice of #hharnisc was that on my local machine /usr/local had not moved, so I just temporarily put $XC_SDK before it on the path, and that seems to work.
some sources:
how to install PIL on Macosx 10.9?
I got this error when running buildout.
I fixed it, first finding the sasl.h file:
mdfind -name sasl.h
then defining the corresponding CFLAGS environment variable:
export CFLAGS="-I/opt/local/include/sasl"
and finally running buildout again.