Building C++ Pybind11 extension with setuptools and CMake generates .so directory - cmake

I am trying to use setuptools to install a C++ library with a Pybind11 interface using CMake. For using CMake with setuptools, I am using the code in the following answer: Extending setuptools extension to use CMake in setup.py?
I am able to build the library by hand with cmake.
Unfortunately however, when executing pip install . in the root directory of my project, the build fails.
While the first call to cmake (self.spawn(['cmake', str(cwd)] + cmake_args)) finishes without any error, executing the second call (self.spawn(['cmake', '--build', '.'] + build_args)) gives me the following error:
/users/thoerman/miniconda3/envs/postproc_np_products/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot open output file /users/thoerman/postproc_np_products/build/lib.linux-x86_64-cpython-37/postproc_ops_cpp.cpython-37m-x86_64-linux-gnu.so: Is a directory
collect2: error: ld returned 1 exit status
gmake[3]: *** [/users/thoerman/postproc_np_products/build/lib.linux-x86_64-cpython-37/postproc_ops_cpp.cpython-37m-x86_64-linux-gnu.so] Error 1
gmake[2]: *** [CMakeFiles/postproc_ops_cpp.dir/all] Error 2
gmake[1]: *** [CMakeFiles/postproc_ops_cpp.dir/rule] Error 2
gmake: *** [postproc_ops_cpp] Error 2
But when running the exact same commands on the command line inside the build_temp directory, everything works just fine.
Does anyone have a hint for me, what might be going wrong?

After further digging into the problem, I found the solution myself.
The problem was with the lines
extdir = pathlib.Path(self.get_ext_fullpath(ext.name))
extdir.mkdir(parents=True, exist_ok=True)
This created a directory for the target to be built. Building the target then failed, since there was already a directory with the same name.
I was able to solve it by replacing the second line as follows:
extdir.parent.mkdir(parents=True, exist_ok=True)

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Making Cmakelist (ros) failure

After installing ros(melodic version), I followed the below steps one by one.
$ mkdir -p catkin_ws/src
$ cd catkin_ws/src
$ catkin_init_workspace
$ cd ..
$ catkin_make
Then error came up like this
CMake Error at CMakeLists.txt:1:
Parse error. Expected a command name, got unquoted argument with text
"/opt/ros/melodic/share/catkin/cmake/toplevel.cmake".
-- Configuring incomplete, errors occurred!
See also "/home/hangilkim/catkin_ws/build/CMakeFiles/CMakeOutput.log".
See also "/home/hangilkim/catkin_ws/build/CMakeFiles/CMakeError.log".
Makefile:320: recipe for target 'cmake_check_build_system' failed
make: *** [cmake_check_build_system] Error 1
Invoking "make cmake_check_build_system" failed
I found that CMakeLists.txt file in 'home/catkin_ws/src' folder exists clearly, but contain only this message.
/opt/ros/melodic/share/catkin/cmake/toplevel.cmake
How can I solve this problem??
Looks like you are trying to compile an already compiled project. So delete the CMakeLists.txt file in 'home/catkin_ws/src' or for safety measures move it to another folder then run catkin_make command on your terminal.

Installing LLReve using Cmake. Unknown BISON_TARGET error

I am getting the following error :
CMake Error at CMakeLists.txt:9 (BISON_TARGET):
Unknown CMake command "BISON_TARGET".
when I run the command :
cmake .. -GNinja
Please tell me what to do. I tried searching on google a lot and thus came up with the additions and finally ran the command :
cmake .. -D LLVM_DIR=/usr/lib/llvm-5.0/cmake/ -D FLEX_EXECUTABLE=/usr/local/Cellar/flex/2.5.37/bin/ -D FLEX_INCLUDE_DIR=/usr/local/Cellar/flex/2.5.37/include/ -D BISON_EXECUTABLE=/usr/bin/bison
but it still shows the same error :(.
Please someone help.
Your error is occurring because the BISON_TARGET function definition has not yet been supplied. This method, as commented, is supplied by FindBISON. The error indicates that either Bison was not found on your system (hopefully, you have it installed), or cmake was ran from the wrong directory. Bison is included in the top-level CMake file via:
find_package(BISON REQUIRED)
This line to include Bison must be called before using the BISON_TARGET CMake function. The LLReve instructions for compiling this repository are explicit about which directory to run the build commands in:
Go to the llreve directory and run
cd reve
mkdir build
cd build
cmake .. -GNinja
ninja
This would run on the CMake file in the llreve/reve directory, not the llreve/reve/reve directory. Please ensure you are running CMake from the correct location, as not running cmake on the top-level CMake file will often yield errors.

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I'm trying to do a clean installation on a PC running Ubuntu 16.04. Originally, GNU Radio was installed by the build-gnuradio script. However, my new USRP board had a different ABI. I decided to redo the installation. Using the script was pretty smooth the last time I used it. After a very long painful day, I got the build to go as far as 100% by issuing the command bash ./build-gnuradio -v -m. However, there is still an error as shown below
Scanning dependencies of target pyuhd
[ 99%] Building CXX object python/CMakeFiles/pyuhd.dir/pyuhd.cpp.o
[100%] Linking CXX shared library libpyuhd.so
[100%] Built target pyuhd
Scanning dependencies of target pyuhd_library
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Traceback (most recent call last):
File "/home/kiruna/grc/uhd/host/build/python/setup.py", line 9, in <module>
from setuptools import setup
ImportError: No module named setuptools
python/CMakeFiles/pyuhd_library.dir/build.make:64: recipe for target 'python/build/timestamp' failed
make[2]: *** [python/build/timestamp] Error 1
CMakeFiles/Makefile2:3997: recipe for target 'python/CMakeFiles/pyuhd_library.dir/all' failed
make[1]: *** [python/CMakeFiles/pyuhd_library.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
UHD build apparently failed
Exiting UHD build
I have used the build-gnuradio so many times in the past but things are quite painful now. Any input will be appreciated.
I had the same problem using pybombs. It seems that the issue happens when you have both python2 and python3 installed. In that case, the cmake script in (UHDSRC)/host/python/CMakeLists.txt erroneously defaults to python3.
I have fixed the issue by replacing the mention of ${PYTHON_EXECUTABLE} around line 68 with ${PYTHON2_EXECUTABLE}
See here: https://twitter.com/f4grx/status/1143620034708815872
Not sure this change is desirable for the upstream project.

project PROJECT called with incorrect number of arguments

when I enter the console:
mkdir build && cd build && cmake .. && make
error occurs:
CMake Error at CMakeLists.txt: 5 (project): project PROJECT called
with incorrect number of arguments
CMake Error at CMakeLists.txt: 19 (find_package): By not providing
"FindQt5Gui.cmake" in CMAKE_MODULE_PATH this project has requested
CMake to find a package configuration file provided by "Qt5Gui", but
CMake did not find one.
Could not find a configuration file provided by "Qt5Gui" with any
of the following names:
Qt5GuiConfig.cmake
qt5gui-config.cmake
Add the installation prefix of "Qt5Gui" to CMAKE_PREFIX_PATH or set
"Qt5Gui_DIR" to a directory containing one of the above files. If
"Qt5Gui" provides a separate development package or SDK, be sure it
has been installed.
on the forums write that this is due to the fact that not installed qt5-defult and gt5-dev-tools, but before the installation and after nothing has changed what to do?

Can't find jemalloc while building MariaDB on Raspbian Wheezy

I have installed the list of Required tools shown on the Build Environment Setup for Linux, including JEMALLOC, on my Raspberry Pi which has Raspbian Wheezy installed, fully updated, and setup for development. I have successfully built some of the listed tools (Bison, CMake 3.7.2). I have gcc and g++ (Raspbian 4.8.2-21rpi3rpi1) 4.8.2.
When I attempt to build mariadb 10.1.22 (master branch from the github repository) using cmake . -DBUILD_CONFIG=mysql_release I get an error:
CMake Error at cmake/jemalloc.cmake:38 (MESSAGE):
jemalloc is not found
Call Stack (most recent call first):
CMakeLists.txt:343 (CHECK_JEMALLOC)
After building JEMALLOC, I installed it into /usr/local using sudo make install. I have export JEMALLOC_PATH=/usr/local in my .bashrc.
I don't understand why CHECK_JEMALLOC is failing to find the correct files. A list of the file locations is:
/usr/local/bin/jemalloc.sh
/usr/local/bin/jemalloc-config
/usr/local/include/jemalloc
/usr/local/include/jemalloc/jemalloc.h
/usr/local/lib/pkgconfig/jemalloc.pc
/usr/local/lib/libjemalloc.so
/usr/local/lib/libjemalloc_pic.a
/usr/local/lib/libjemalloc.so.2
/usr/local/lib/libjemalloc.a
/usr/local/share/doc/jemalloc
/usr/local/share/doc/jemalloc/jemalloc.html
/usr/local/share/man/man3/jemalloc.3
I can attach a link to the CMake configure log, error log, and terminal output if needed.
UPDATE
I tried using just cmake . and the configuration part worked, but the make failed with the following error:
/home/user/Downloads/mariadb/server/storage/mroonga/vendor/groonga/lib/expr.c:6816:7: note: in expansion of macro ‘GRN_PTR_POP’
GRN_PTR_POP(&keywords, keyword);
^
cc: internal compiler error: Killed (program cc1)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.
storage/mroonga/vendor/groonga/lib/CMakeFiles/libgroonga.dir/build.make:257: recipe for target 'storage/mroonga/vendor/groonga/lib/CMakeFiles/libgroonga.dir/expr.c.o' failed
make[2]: *** [storage/mroonga/vendor/groonga/lib/CMakeFiles/libgroonga.dir/expr.c.o] Error 4
make[2]: Leaving directory '/home/user/Downloads/mariadb/server'
CMakeFiles/Makefile2:4420: recipe for target 'storage/mroonga/vendor/groonga/lib/CMakeFiles/libgroonga.dir/all' failed
make[1]: *** [storage/mroonga/vendor/groonga/lib/CMakeFiles/libgroonga.dir/all] Error 2
make[1]: Leaving directory '/home/user/Downloads/mariadb/server'
Makefile:152: recipe for target 'all' failed
make: *** [all] Error 2