Cannot install under OSX Mojave (10.14) using pip and python 3.7

[misan]

I have installed octomap before but once I type
$ pip3 install python-fcl

It fails with this output:

Collecting python-fcl
Using cached https://files.pythonhosted.org/packages/d6/1a/51e9a3cf8473f297226396ad508702483f4fe3df9bb60676b35d2aca340d/python-fcl-0.0.12.tar.gz
Requirement already satisfied: numpy in /Users/misan/Library/Python/3.7/lib/python/site-packages (from python-fcl) (1.16.4)
Requirement already satisfied: cython in /Users/misan/Library/Python/3.7/lib/python/site-packages (from python-fcl) (0.29.10)
Building wheels for collected packages: python-fcl
Building wheel for python-fcl (setup.py) ... error
ERROR: Complete output from command /usr/local/opt/python/bin/python3.7 -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/rz/kw6z5q015bx5_zhls77kznz00000gn/T/pip-install-zz_36jyd/python-fcl/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/rz/kw6z5q015bx5_zhls77kznz00000gn/T/pip-wheel-w3h9lffv --python-tag cp37:
ERROR: running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/fcl
copying fcl/collision_data.py -> build/lib.macosx-10.14-x86_64-3.7/fcl
copying fcl/version.py -> build/lib.macosx-10.14-x86_64-3.7/fcl
copying fcl/init.py -> build/lib.macosx-10.14-x86_64-3.7/fcl
running build_ext
cythoning fcl/fcl.pyx to fcl/fcl.cpp
building 'fcl.fcl' extension
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/fcl
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/include -I/usr/local/include -I/usr/include/eigen3 -I/Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.2_2/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c fcl/fcl.cpp -o build/temp.macosx-10.14-x86_64-3.7/fcl/fcl.o -std=c++11
In file included from fcl/fcl.cpp:619:
In file included from /Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with "
^
fcl/fcl.cpp:627:10: fatal error: 'fcl/data_types.h' file not found
#include "fcl/data_types.h"
^~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.
error: command 'clang' failed with exit status 1

ERROR: Failed building wheel for python-fcl
Running setup.py clean for python-fcl
Failed to build python-fcl
Installing collected packages: python-fcl
Running setup.py install for python-fcl ... error
ERROR: Complete output from command /usr/local/opt/python/bin/python3.7 -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/rz/kw6z5q015bx5_zhls77kznz00000gn/T/pip-install-zz_36jyd/python-fcl/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/rz/kw6z5q015bx5_zhls77kznz00000gn/T/pip-record-oh_p8l97/install-record.txt --single-version-externally-managed --compile:
ERROR: running install
running build
running build_py
creating build
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/fcl
copying fcl/collision_data.py -> build/lib.macosx-10.14-x86_64-3.7/fcl
copying fcl/version.py -> build/lib.macosx-10.14-x86_64-3.7/fcl
copying fcl/init.py -> build/lib.macosx-10.14-x86_64-3.7/fcl
running build_ext
skipping 'fcl/fcl.cpp' Cython extension (up-to-date)
building 'fcl.fcl' extension
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/fcl
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/include -I/usr/local/include -I/usr/include/eigen3 -I/Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.2_2/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c fcl/fcl.cpp -o build/temp.macosx-10.14-x86_64-3.7/fcl/fcl.o -std=c++11
In file included from fcl/fcl.cpp:619:
In file included from /Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/Users/misan/Library/Python/3.7/lib/python/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with "
^
fcl/fcl.cpp:627:10: fatal error: 'fcl/data_types.h' file not found
#include "fcl/data_types.h"
^~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.
error: command 'clang' failed with exit status 1
----------------------------------------
ERROR: Command "/usr/local/opt/python/bin/python3.7 -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/rz/kw6z5q015bx5_zhls77kznz00000gn/T/pip-install-zz_36jyd/python-fcl/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/rz/kw6z5q015bx5_zhls77kznz00000gn/T/pip-record-oh_p8l97/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/rz/kw6z5q015bx5_zhls77kznz00000gn/T/pip-install-zz_36jyd/python-fcl/

[misan]

Ok, I need to install fcl first, and before that libccd ... pip does not do that apparently :-(

[misan]

Ok, I closed it too early. I am still stuck at the same point now that I have installed eigen, libccd and fcl.

And I am in fact not able to see any data_types.h in fcl include files.

[misan]

I guess there is a versioning problem.

$ brew install fcl

did the trick for me.

[menglaili]

I have installed eigen, fcl using Homebrew and libccd using Makefile, but I still face the same problem. What versions do you choose for these dependencies?

[Amar1729]

This isn't in the bullets under FCL's releases, but it looks like in version 0.6.0 data_types.h was renamed to common/types.h.

@menglaili I think when this issue was originally opened, homebrew-core had FCL version 0.5.0 (whereas current is 0.6.1).

Installing python-fcl works for me if I checkout back to fcl@0.5.0 with homebrew and build that, but I guess this library should probably be updated to reflect the new file location.

Looks like there are two open PRs for updating to 0.6.0: https://github.com/BerkeleyAutomation/python-fcl/pulls

[Aniwax]

Why is this issue closed? Since python-fcl doesn't work with fcl@0.6.0 yet?
Btw, brew install fcl@0.5.0 is not working for me. Can someone give me a hint on how to install the 0.5.0 version from the zip file?

[Amar1729]

@Aniwax I literally checked out the homebrew repo back in time --

1. cd to homebrew's repo (typically /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula)

2. determine the last commit for fcl.rb 5.x (git log -- fcl.rb and read the log messages) and checkout to that commit

• in this case i used git checkout 75dc086c11

3. install fcl normally brew install fcl
   a. pin the formula so it doesn't auto upgrade (brew pin fcl)

4. checkout back to master (git checkout master)

This is a bit of a hack since homebrew no longer keeps old versions except for very highly-used formuale.

[Amar1729]

This issue is probably still relevant until pull #20 or #21 are finished.

[Aniwax]

Thanks a lot! @Amar1729