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stack-of-tasks / pinocchio

A fast and flexible implementation of Rigid Body Dynamics algorithms and their analytical derivatives
http://stack-of-tasks.github.io/pinocchio/
BSD 2-Clause "Simplified" License
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Mac Pinocchio install failure #709

Closed ddliu365 closed 5 years ago

ddliu365 commented 5 years ago

I would like to install Pinocchio on Mac. When I try to import Pinocchio in the python2, I met the following error:

ImportError: dlopen(/usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so, 2): Symbol not found: __ZN5boost6system16generic_categoryEv Referenced from: /usr/local/lib/libhpp-fcl.dylib Expected in: /usr/local/opt/boost/lib/libboost_system-mt.dylib in /usr/local/lib/libhpp-fcl.dylib

I guess this is caused by the library of hpp-fcl or the boost, though I have tried many times to install these two packages with latest home-brew. Can you help me out?

jcarpent commented 5 years ago

What is your Mac version?

jcarpent commented 5 years ago

I have updated the brew formula for pinocchio and hpp-fcl. @ddliugit Can you tell me if everything goes fine now?

ddliu365 commented 5 years ago

Mac Mojave version:10.14.3

Thanks, I will try it again

ddliu365 commented 5 years ago

I tried it just now and found the problem changed.

I guess there exists problem in hpp-fcl library.

The following is the log in my terminal.

Can you help me find the problem?

My Mac version is Mojave 10.14.3

$ python2 Python 2.7.16 (default, Mar 4 2019, 09:01:38) [GCC 4.2.1 Compatible Apple LLVM 10.0.0 (clang-1000.11.45.5)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import pinocchio Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/site-packages/pinocchio/init.py", line 6, in from pinocchio.robot_wrapper import RobotWrapper File "/usr/local/lib/python2.7/site-packages/pinocchio/robot_wrapper.py", line 5, in from . import libpinocchio_pywrap as pin ImportError: dlopen(/usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so, 2): Symbol not found: __ZN3fcl8BVHModelINS_6OBBRSSEE10beginModelEii Referenced from: /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so Expected in: /usr/local/lib/libhpp-fcl.dylib in /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so

jcarpent commented 5 years ago

can you do brew reinstall hpp-fcl?

ddliu365 commented 5 years ago

Yes, I tried it just now

The problem still exists and this is the log in the system

$ brew reinstall hpp-fcl ==> Reinstalling gepetto/gepetto/hpp-fcl ==> Downloading https://github.com/humanoid-path-planner/hpp-fcl/releases/downlo Already downloaded: /Users/dongdong/Library/Caches/Homebrew/downloads/6d8c8e604ca0a47222d1ff471ebaf21f0597701a7dd83742eb7e7e9338c8bf96--hpp-fcl-1.0.1.mojave.bottle.1.tar.gz ==> Pouring hpp-fcl-1.0.1.mojave.bottle.1.tar.gz 🍺 /usr/local/Cellar/hpp-fcl/1.0.1: 1,666 files, 13.9MB Dongdongs-MacBook-Pro:~ dongdong$ python2 Python 2.7.16 (default, Mar 4 2019, 09:01:38) [GCC 4.2.1 Compatible Apple LLVM 10.0.0 (clang-1000.11.45.5)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import pinocchio Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/site-packages/pinocchio/init.py", line 6, in from pinocchio.robot_wrapper import RobotWrapper File "/usr/local/lib/python2.7/site-packages/pinocchio/robot_wrapper.py", line 5, in from . import libpinocchio_pywrap as pin ImportError: dlopen(/usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so, 2): Symbol not found: __ZN3fcl8BVHModelINS_6OBBRSSEE10beginModelEii Referenced from: /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so Expected in: /usr/local/lib/libhpp-fcl.dylib in /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so

ddliu365 commented 5 years ago

What is this problem

Did you test in MAC Mojave

jcarpent commented 5 years ago

Yes, I'm on Mojave. The problem is that you do not have the missing hpp::fcl namespace.

jcarpent commented 5 years ago

Can you try to reinstall from source both hpp-fcl and pinocchio: brew reinstall --build-from-source hpp-fcl and brew reinstall --build-from-source pinocchio

jcarpent commented 5 years ago

In fact, I think you need to reinstall pinocchio too. This is the problem here.

ddliu365 commented 5 years ago

I just tried to reinstall and build from source, but the same problem happened again

The log info from the terminal:

$ python2 Python 2.7.16 (default, Mar 4 2019, 09:01:38) [GCC 4.2.1 Compatible Apple LLVM 10.0.0 (clang-1000.11.45.5)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import pinocchio Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/site-packages/pinocchio/init.py", line 6, in from pinocchio.robot_wrapper import RobotWrapper File "/usr/local/lib/python2.7/site-packages/pinocchio/robot_wrapper.py", line 5, in from . import libpinocchio_pywrap as pin ImportError: dlopen(/usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so, 2): Symbol not found: __ZN3fcl8BVHModelINS_6OBBRSSEE10beginModelEii Referenced from: /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so Expected in: /usr/local/lib/libhpp-fcl.dylib in /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so

ddliu365 commented 5 years ago

Does it work well on your Mac Mojave?

$ brew reinstall --build-from-source hpp-fcl ==> Reinstalling gepetto/gepetto/hpp-fcl ==> Downloading https://github.com/humanoid-path-planner/hpp-fcl/releases/downlo ==> Downloading from https://github-production-release-asset-2e65be.s3.amazonaws ######################################################################## 100.0% ==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG ==> make ==> make test ==> make install 🍺 /usr/local/Cellar/hpp-fcl/1.0.1: 833 files, 10.6MB, built in 2 minutes 21 seconds Dongdongs-MacBook-Pro:~ dongdong$ brew reinstall --build-from-source pinocchio ==> Reinstalling gepetto/gepetto/pinocchio ==> Downloading https://github.com/stack-of-tasks/pinocchio/releases/download/v2 Already downloaded: /Users/dongdong/Library/Caches/Homebrew/downloads/b54092714b1ba96c6aa78ae3a09f0223fcd1c8f2753c536f01b2e0bddc3079fa--pinocchio-2.1.0.tar.gz ==> Patching ==> cmake .. -DCMAKE_C_FLAGS_RELEASE=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG ==> make ==> make install Warning: gepetto/gepetto/pinocchio dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. Error: The brew link step did not complete successfully The formula built, but is not symlinked into /usr/local Could not symlink include/pinocchio/algorithm/aba-derivatives.hpp Target /usr/local/include/pinocchio/algorithm/aba-derivatives.hpp already exists. You may want to remove it: rm '/usr/local/include/pinocchio/algorithm/aba-derivatives.hpp'

To force the link and overwrite all conflicting files: brew link --overwrite pinocchio

To list all files that would be deleted: brew link --overwrite --dry-run pinocchio

Possible conflicting files are: /usr/local/include/pinocchio/algorithm/aba-derivatives.hpp /usr/local/include/pinocchio/algorithm/aba-derivatives.hxx /usr/local/include/pinocchio/algorithm/aba.hpp /usr/local/include/pinocchio/algorithm/aba.hxx /usr/local/include/pinocchio/algorithm/center-of-mass.hpp /usr/local/include/pinocchio/algorithm/center-of-mass.hxx /usr/local/include/pinocchio/algorithm/centroidal-derivatives.hpp /usr/local/include/pinocchio/algorithm/centroidal-derivatives.hxx /usr/local/include/pinocchio/algorithm/centroidal.hpp /usr/local/include/pinocchio/algorithm/centroidal.hxx /usr/local/include/pinocchio/algorithm/check.hpp /usr/local/include/pinocchio/algorithm/check.hxx /usr/local/include/pinocchio/algorithm/cholesky.hpp /usr/local/include/pinocchio/algorithm/cholesky.hxx /usr/local/include/pinocchio/algorithm/compute-all-terms.hpp /usr/local/include/pinocchio/algorithm/copy.hpp /usr/local/include/pinocchio/algorithm/crba.hpp 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/usr/local/include/pinocchio/algorithm/kinematics.hxx /usr/local/include/pinocchio/algorithm/regressor.hpp /usr/local/include/pinocchio/algorithm/regressor.hxx /usr/local/include/pinocchio/algorithm/rnea-derivatives.hpp /usr/local/include/pinocchio/algorithm/rnea-derivatives.hxx /usr/local/include/pinocchio/algorithm/rnea.hpp /usr/local/include/pinocchio/algorithm/rnea.hxx /usr/local/include/pinocchio/bindings/python/algorithm/algorithms.hpp /usr/local/include/pinocchio/bindings/python/fwd.hpp /usr/local/include/pinocchio/bindings/python/multibody/data.hpp /usr/local/include/pinocchio/bindings/python/multibody/fcl/collision-geometry.hpp /usr/local/include/pinocchio/bindings/python/multibody/fcl/collision-result.hpp /usr/local/include/pinocchio/bindings/python/multibody/fcl/contact.hpp /usr/local/include/pinocchio/bindings/python/multibody/fcl/distance-result.hpp /usr/local/include/pinocchio/bindings/python/multibody/frame.hpp 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/usr/local/lib/python2.7/site-packages/pinocchio/shortcuts.py /usr/local/lib/python2.7/site-packages/pinocchio/utils.py ==> Summary 🍺 /usr/local/Cellar/pinocchio/2.1.0: 1,845 files, 31.2MB, built in 8 minutes 49 seconds Dongdongs-MacBook-Pro:~ dongdong$ python2 Python 2.7.16 (default, Mar 4 2019, 09:01:38) [GCC 4.2.1 Compatible Apple LLVM 10.0.0 (clang-1000.11.45.5)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import pinocchio Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/site-packages/pinocchio/init.py", line 6, in from pinocchio.robot_wrapper import RobotWrapper File "/usr/local/lib/python2.7/site-packages/pinocchio/robot_wrapper.py", line 5, in from . import libpinocchio_pywrap as pin ImportError: dlopen(/usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so, 2): Symbol not found: __ZN3fcl8BVHModelINS_6OBBRSSEE10beginModelEii Referenced from: /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so Expected in: /usr/local/lib/libhpp-fcl.dylib in /usr/local/lib/python2.7/site-packages/pinocchio/libpinocchio_pywrap.so

jcarpent commented 5 years ago

As written in the log, you forgot to brew link --overwrite pinocchio. Please do it and try it again.

ddliu365 commented 5 years ago

Yes, it worked!!

Thanks a lot.