Undefined symbol error in libpinocchio_pywrap.so

[spykspeigel]

Hello, I tried a source installation. But received the following error

  Linking CXX executable test-cpp-serialization
/usr/bin/c++   -pedantic -Wno-long-long -Wall -Wextra -Wcast-align -Wcast-qual -Wformat -Wwrite-strings -Wconversion  -O3 -DNDEBUG  -rdynamic CMakeFiles/test-cpp-serialization.dir/serialization.cpp.o  -o test-cpp-serialization  -Wl,-rpath,/home/sp/Documents/pinocchio/build/src ../src/libpinocchio.so.2.6.4 -lboost_unit_test_framework -lboost_filesystem -lboost_system -lboost_serialization -lurdfdom_sensor -lurdfdom_model_state -lurdfdom_model -lurdfdom_world /usr/lib/x86_64-linux-gnu/libconsole_bridge.so.0.4 
/usr/bin/ld: CMakeFiles/test-cpp-serialization.dir/serialization.cpp.o: in function `__static_initialization_and_destruction_0(int, int) [clone .constprop.0]':
serialization.cpp:(.text.startup+0x1c6): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::unit_test::decorator::collector&)'
/usr/bin/ld: serialization.cpp:(.text.startup+0x252): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
/usr/bin/ld: serialization.cpp:(.text.startup+0x2fa): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
/usr/bin/ld: serialization.cpp:(.text.startup+0x39a): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
/usr/bin/ld: serialization.cpp:(.text.startup+0x43a): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
/usr/bin/ld: serialization.cpp:(.text.startup+0x4da): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
/usr/bin/ld: CMakeFiles/test-cpp-serialization.dir/serialization.cpp.o:serialization.cpp:(.text.startup+0x57a): more undefined references to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' follow
collect2: error: ld returned 1 exit status
make[2]: *** [unittest/CMakeFiles/test-cpp-serialization.dir/build.make:97: unittest/test-cpp-serialization] Error 1

On turning off Build_unit_test, the compilation was complete. But on importing Pinocchio I receive the following import error.

ImportError: /usr/local/lib/libpinocchio.so.2.6.4: undefined symbol: _ZN5boost6system15system_categoryEv

The dependencies with, ldd /usr/local/lib/libpinocchio.so.2.6.4 are

    linux-vdso.so.1 (0x00007fffaa9b3000)
    libboost_filesystem.so.1.71.0 => /lib/x86_64-linux-gnu/libboost_filesystem.so.1.71.0 (0x00007f2ceca80000)
    liburdfdom_model.so.1.0 => /lib/x86_64-linux-gnu/liburdfdom_model.so.1.0 (0x00007f2ceca5b000)
    libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f2cec879000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f2cec85e000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2cec66c000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2cec647000)
    libtinyxml.so.2.6.2 => /lib/x86_64-linux-gnu/libtinyxml.so.2.6.2 (0x00007f2cec62f000)
    libconsole_bridge.so.0.4 => /lib/x86_64-linux-gnu/libconsole_bridge.so.0.4 (0x00007f2cec629000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2cec4da000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f2cecafe000)

I suspect there is an issue with the libboost but not sure about the specific issue. Any help is greatly appreciated.

[jcarpent]

At first glance, you have several installations of Pinocchio on your computer. Why do you want to install it from source? In the meantime, you are not the first one to encounter such installation issues which is mostly due to a dirty install setting. I invite you to look at the other issues in GitHub. To check the several install, just do: locate libpinocchio.so

[spykspeigel]

Hey @jcarpent. Yes, I had a binary installation. I am working on a new stateclass in Crocoddyl library and for this I wanted python binding of dIntegrateTransport. There is no binding related to dIntegrateTransport in Pinocchio. Is it not exposed for any specific reason? For this requirement, I did add the corresponding bindings but faced the above issue.

[jcarpent]

So just remove it and let's play. The dIntegrateTransport will be added soon. We already have a fix for that thanks to @ManifoldFR.

[jcarpent]

I think we can now close the issue which seems to be solved.

[cmastalli]

The dIntegrateTransport will be added soon. We already have a fix for that thanks to @ManifoldFR.

This is great! These bindings are blocking us, we are keen to implement it (or support you) ourselves if this will take time to be available. Could you tell us when you think it will be available (in devel branch)?

Many thanks ;)

[proyan]

The python bindings of dIntegrateTransport are already present in the main lib: https://github.com/stack-of-tasks/pinocchio/blob/master/bindings/python/multibody/liegroups.hpp#L194

Is there something specific that you are searching @spykspeigel @cmastalli ?

[cmastalli]

The python bindings of dIntegrateTransport are already present in the main lib: https://github.com/stack-of-tasks/pinocchio/blob/master/bindings/python/multibody/liegroups.hpp#L194

Is there something specific that you are searching @spykspeigel @cmastalli ?

We need the bindings of the joint algo: https://github.com/stack-of-tasks/pinocchio/blob/a1df23c2f183d84febdc2099e5fbfdbd1fc8018b/src/algorithm/joint-configuration.hxx#L174-L220, which I think it should be implemented here: https://github.com/stack-of-tasks/pinocchio/blob/master/bindings/python/algorithm/expose-joints.cpp

[ManifoldFR]

Hi, I cherry-picked a commit from my working branch and proposed PR #1572 to add this functionality.

[spykspeigel]

Thanks. :)