Cmake is not able to find Python-libraries

Question

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?

Tried and it recognized but still : `Could NOT find PythonLibs (missing: PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS) ` — Amit Pal, Jun 12 '14 at 00:31
Could you please include the code of the rdkit root CMakeLists.txt file to your question? That might help. — Bertrand Moreau, Jul 16 '14 at 08:53

score 75 · Answer 1 · edited Jan 06 '23 at 08:30

75

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.

edited Jan 06 '23 at 08:30

joe

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answered Jun 30 '16 at 11:36

Ivan De Paz Centeno

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print(sysconfig.get_config_var('LIBDIR'))" prints /opt/conda/lib, but then I get WARNING: Target "something-something" requests linking to directory "/opt/conda/lib". Targets may link only to libraries. CMake is dropping the item. - Do we need to give -DPYTHON_LIBRARY the path to the .so libpython? – Mr.WorshipMe Aug 20 '16 at 22:03
5

@Mr.WorshipMe yes, I changed the command to give the path to the .so like so: `-DPYTHON_LIBRARY=$(python -c "import distutils.sysconfig as sysconfig; import os; print(os.path.join(sysconfig.get_config_var('LIBDIR'), sysconfig.get_config_var('LDLIBRARY')))")` – kgully Nov 03 '16 at 18:03
For anaconda in particular, this worked for me (and will hopefully generalize more easily): https://github.com/jkhoogland/FindPythonAnaconda (though I had to make two small changes -- they're both in my GitHub fork if upstream doesn't quite work for you either) – Braham Snyder Sep 13 '17 at 01:06
This is the best answer, as it automatically adjusts to the current python (`which python`) and works seamlessly when a conda env is active). – Brent Faust May 04 '18 at 22:55
Note (I hope it helps M1 Mac people using Cmake with Python 3): in my case in order to make my specific problem work I needed to do `DPYTHON3_LIBRARY` and `DPYTHON3_INCLUDE_DIR`. It didn't work without the 3. – Melvin Roest Aug 24 '21 at 20:04
For anybody else seeing the deprecation warning for `distutils.sysconfig`. You can use `sysconfig` and call `sysconfig.get_path('include')` for the -DPYTHON_INCLUDE_DIR and `sysconfig.get_config_var('LIBDIR')` – Joseph Bradshaw Jul 19 '22 at 22:46

score 44 · Answer 2 · edited Feb 17 '22 at 11:07

44

For me this is helpful:

# if using python2
apt-get install python-dev

# if using python3
apt-get install python3-dev

edited Feb 17 '22 at 11:07

Yongkin

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answered Apr 07 '15 at 20:18

Oleksandr Mosur

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2

For me (on Centos7) this line solved the issue: `yum install python34-devel` – Agnis May 04 '17 at 14:07
This worked for me, without any of the cmake arguments (`-DPYTHON_LIBRARY` etc) suggested by the other answers. I had `python-dev`, but had forgotten `python3-dev`. – tsbertalan Feb 03 '19 at 03:51
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Very bad answer. It's like, if it doesn't work, try to install everything. It's either python2 or python3 you need... (Now in 2020, better update your answer as python2 is deprecated) – jaques-sam Oct 27 '20 at 10:04
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This should be marked as the correct answer. – KLiFF Jul 28 '21 at 09:47
This solved the issue for me. – Yishai E Mar 02 '22 at 09:46

score 21 · Answer 3 · edited Jan 10 '18 at 12:10

21

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.

edited Jan 10 '18 at 12:10

Iain Haslam

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answered Apr 15 '15 at 17:50

Chris Lyon

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This really needs to be mentioned in the documentation for opencv installs. Also they could be a little more helpful about explaining the available cmake options when building from source. http://docs.opencv.org/master/d7/d9f/tutorial_linux_install.html – May 14 '17 at 23:18

score 19 · Answer 4 · answered Jan 13 '18 at 16:25

19

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`

answered Jan 13 '18 at 16:25

Lane Rettig

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Thanks! I also found that github page but I was only setting the PYTHON_EXECUTABLE:FILEPATH and that didn't work. Your solution solved my issue when trying to build OpenVDB on MacOSX (Mojave). – nantille Jun 29 '19 at 12:47
Thanks so much, I can't find libpython-x.so and failed to manual compile&install opencv-python, and this way solved my prolem – Sailist Mar 10 '21 at 03:58

score 15 · Answer 5 · answered Jun 15 '15 at 14:31

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.

And do not forget clean all cmake caches firstly! – acgtyrant May 19 '16 at 07:49 — acgtyrant, May 19 '16 at 07:49
@acgtyrant how do you do that? cmake clean? – KansaiRobot Apr 19 '21 at 07:22 — KansaiRobot, Apr 19 '21 at 07:22

score 10 · Answer 6 · answered Feb 09 '15 at 16:25

10

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.

answered Feb 09 '15 at 16:25

Patrizio Bertoni

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This was the problem for my 14.04 Ubuntu system. I fixed it by installing a newer cmake version (https://askubuntu.com/a/945589/187411) – UTF_or_Death Jun 19 '18 at 19:06
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I solved the problem by `Remember to clean CMakeCache.txt too.` many thanks Patrizio. in the mbec-cli2 CMake (not found jinja2, intelhex, prettytable). – kuri65536 Apr 30 '21 at 23:02

score 7 · Answer 7 · answered Nov 17 '15 at 14:47

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\\"

Will this also work if I have both 32 and 64 bit versions installed at the same time and want to build both 32 and 64 bit C++ binaries? — Damian, Aug 02 '18 at 09:32

score 2 · Answer 8 · answered Nov 19 '18 at 03:54

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.

score 2 · Answer 9 · answered Dec 13 '21 at 19:41

2

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

answered Dec 13 '21 at 19:41

Dylan Kerler

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score 1 · Answer 10 · answered Jul 03 '18 at 06:51

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)

score 1 · Answer 11 · answered Oct 28 '19 at 21:34

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/

score 1 · Answer 12 · answered Aug 10 '22 at 09:47

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"
        ...

score 0 · Answer 13 · answered Jun 21 '21 at 03:07

0

Maybe below command line works for you if all of above methods didn't work.

sudo apt-get install cython cython3

answered Jun 21 '21 at 03:07

WangYang

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score 0 · Answer 14 · answered Apr 15 '22 at 07:55

0

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

answered Apr 15 '22 at 07:55

mmerle

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Cmake is not able to find Python-libraries

14 Answers14

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